Re: [ccp4bb] CCP4BB Digest - 7 Jun 2024 to 8 Jun 2024 (#2024-142)

[Simon Vecchioni]

Paul and Lucrezia,

Restarting Coot seems to be the magic bullet to restore atom fixing. This
works for the tutorials and the DNA model I'm working on.

Thanks for your help,
Simon


>
> Date:Sat, 8 Jun 2024 18:47:22 +0100
> From:Paul Emsley 
> Subject: Re: Coot 1.1 General Tools
>
>
> Re 3:
>
>
> Starting from a fresh coot:
>
> Calculate -> Load Tutorial Model and Data
>
> Draw Molecule -> Go To Atom...
>
> Click on the triangle of Chain A to open Chain A
>
> Double Click on "A 4 GLY"
>
> Shift Right Mouse to Zoom in
>
> Fixed Atoms... -> Fix Atom
>
> [An anchor appears]
>
> - mci: mark_atom_as_fixed() [spec: model 1 "A"4
> "" " CA " ""] 1
> INFO:: [spec: model 1 "A"4 "" " CA " ""] marked as fixed
>
>
>
>



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Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

[CCP4BB]

Hi Nick

I noticed this today when I was researching the differences between mmCIF and 
modelCIF - but thanks anyway. 

I haven't tried running it yet, but the important thing for me is to be able to 
convert my bare-bones PDB format files to something that AlphaFill will accept 
- and as the PDB-REDO team's pdb2cif does the job, I think my search is over.

In fact, better than that - it seems that the latest version of AlphaFill reads 
"my" PDB files correctly, so I should be able to avoid the conversion step. 

Harry
--
Dr Harry Powell

> On 26 Feb 2024, at 17:54, Nicholas Clark 
>  wrote:
> 
> Hi Harry,
> 
> I did stumble upon this python mmCIF handler for modelCIF: 
> 
> https://github.com/ihmwg/python-modelcif/blob/main/examples/README.md
> 
> 
> Maybe this will have something of use to your efforts? 
> 
> Best,
> 
> Nick Clark
> 
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
> 
> Cell: 716-830-1908
> 
> 
>> On Mon, Feb 26, 2024 at 7:16 AM Harry Powell 
>> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>> Hi folks
>> 
>> I’ve made considerable progress in getting to the bottom of this problem. 
>> From what I can gather, AlphaFold writes “modelCIF”, which is not quite the 
>> same as “mmCIF”, and just saying “CIF” is not unambiguous. So I guess I 
>> should have been more aware of this when posting my original question.
>> 
>> With regard to the programs mentioned (note these are not all my analyses, 
>> so please don’t shoot the messenger!) - 
>> 
>> * Pymol produces a file which is some way from “standard” and would need 
>> work to make it usable (so something for Schroedinger to work on, perhaps).
>> 
>> * Coot *almost* produces a file that can be used  (authors aware).
>> 
>> * Gemmi is also close, but no cigar  (authors aware).
>> 
>> * I’d guess that Maxit was last revised many years before modelCIF was 
>> introduced so I don’t think this would be a fruitful path to follow (the 
>> build failed on my newly installed Linux because it was an unrecognised 
>> system, and the most recent binary was built in 2008).
>> 
>> Many thanks to everyone who took the time to read and answer my question!
>> 
>> Harry
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

[Nicholas Clark]

Hi Harry,

I did stumble upon this python mmCIF handler for modelCIF:

https://github.com/ihmwg/python-modelcif/blob/main/examples/README.md


Maybe this will have something of use to your efforts?

Best,

Nick Clark

Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203

Cell: 716-830-1908


On Mon, Feb 26, 2024 at 7:16 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi folks
>
> I’ve made considerable progress in getting to the bottom of this problem.
> From what I can gather, AlphaFold writes “modelCIF”, which is not quite the
> same as “mmCIF”, and just saying “CIF” is not unambiguous. So I guess I
> should have been more aware of this when posting my original question.
>
> With regard to the programs mentioned (note these are not all my analyses,
> so please don’t shoot the messenger!) -
>
> * Pymol produces a file which is some way from “standard” and would need
> work to make it usable (so something for Schroedinger to work on, perhaps).
>
> * Coot *almost* produces a file that can be used  (authors aware).
>
> * Gemmi is also close, but no cigar  (authors aware).
>
> * I’d guess that Maxit was last revised many years before modelCIF was
> introduced so I don’t think this would be a fruitful path to follow (the
> build failed on my newly installed Linux because it was an unrecognised
> system, and the most recent binary was built in 2008).
>
> Many thanks to everyone who took the time to read and answer my question!
>
> Harry
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi folks

I’ve made considerable progress in getting to the bottom of this problem. From 
what I can gather, AlphaFold writes “modelCIF”, which is not quite the same as 
“mmCIF”, and just saying “CIF” is not unambiguous. So I guess I should have 
been more aware of this when posting my original question.

With regard to the programs mentioned (note these are not all my analyses, so 
please don’t shoot the messenger!) - 

* Pymol produces a file which is some way from “standard” and would need work 
to make it usable (so something for Schroedinger to work on, perhaps).

* Coot *almost* produces a file that can be used  (authors aware).

* Gemmi is also close, but no cigar  (authors aware).

* I’d guess that Maxit was last revised many years before modelCIF was 
introduced so I don’t think this would be a fruitful path to follow (the build 
failed on my newly installed Linux because it was an unrecognised system, and 
the most recent binary was built in 2008).

Many thanks to everyone who took the time to read and answer my question!

Harry



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Re: [ccp4bb] [ccp4bb] mmCIF files from PDB format for AlphaFill

[Harry Powell]

Hi Nick

doesn’t look encouraging - 

> ~/maxit/maxit-v8.120-prod-bin-linux/bin/maxit-v8.01-O -i 1A9W_A.pdb -o 1
> Initial filter libaray failed

No need to worry - since the pdb2cif from the pdb-redo team works, and they’re 
the ones who produce AlphaFill, they can always help out if (when) things go 
wrong!

best wishes and thanks again 

Harry

> On 23 Feb 2024, at 14:00, Nicholas Clark 
>  wrote:
> 
> Hi Harry,
> 
> Unfortunately, I did not see that the latest binary update was from 2008. I 
> do not have access to any newer binaries for Linux, as I'm on MacOS. 
> 
> Maybe you can use the MineProt software from the quote I mentioned previously 
> to (in a roundabout way) accomplish the CIF file generation?
> 
> "“Huiwenke:
> 
> MineProt (https://github.com/huiwenke/MineProt) can be used to curate 
> AlphaFold predictions, where PDBs are converted into CIFs using MAXIT 
> (https://sw-tools.rcsb.org/apps/MAXIT/index.html). The generated CIF files 
> support Mol* visualization and downstream analysis such as AlphaFill 
> (https://github.com/PDB-REDO/alphafill).
> Another possible option is to use MAXIT directly, while it needs several 
> additional steps to make generated CIF files support older versions of Mol*. 
> Please refer to 
> https://github.com/huiwenke/MineProt/blob/master/web/api/pdb2alphacif/index.php.”;
> 
> Best,
> 
> Nick
> 
> 
> 
> -- Forwarded message -
> From: Nicholas Clark 
> Date: Fri, Feb 23, 2024 at 8:03 AM
> Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
> To: Harry Powell 
> Cc: Harry Powell 
> 
> 
> Hi Harry,
> 
> MAXIT binaries are located here:
> 
> https://sw-tools.rcsb.org/apps/MAXIT/binary.html
> 
> Best,
> 
> Nick
> 
> 
> Nicholas D. Clark (He/Him)
> PhD Candidate
> Malkowski Lab
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street, RM 5130
> Buffalo, NY 14203
> 
> Cell: 716-830-1908
> 
> 
> On Fri, Feb 23, 2024 at 7:58 AM Harry Powell  
> wrote:
> Hi Nick
> 
> Thanks for responding, but see my earlier reply to Avinash - the build 
> doesn’t like my brand-new, hot off the production line Linux and the location 
> of pre-built exes is not obvious.
> 
> best wishes
> 
> Harry
> 
> > On 23 Feb 2024, at 12:43, Nicholas Clark 
> >  wrote:
> > 
> > Hi Harry,
> > 
> > Have you tried MAXIT from the PDB? It can be installed locally:
> > 
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsw-tools.rcsb.org%2Fapps%2FMAXIT%2Findex.html=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2f0b5620024b4430110208dc346f20b3%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638442899115806976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=W3%2BzEKkB1%2BpJznVNIUjTDqMcww3v3YxylxULJCOLgf4%3D=0
> > 
> > Best,
> > 
> > Nick Clark
> > 
> > Nicholas D. Clark (He/Him)
> > PhD Candidate
> > Malkowski Lab
> > University at Buffalo
> > Department of Structural Biology
> > Jacob's School of Medicine & Biomedical Sciences
> > 955 Main Street, RM 5130
> > Buffalo, NY 14203
> > 
> > Cell: 716-830-1908
> > 
> > 
> > On Fri, Feb 23, 2024 at 7:36 AM Harry Powell 
> > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> > Hi Martin, Marcin, Arturo, Avinash
> > 
> > First off, I’m **NOT** saying that there’s anything wrong with the CIF 
> > files produced by these routes - just that AlphaFill doesn’t like them (it 
> > *does* like CIFs from AlphaFold - 
> > 
> > > alphafill process alphafold.cif filled.cif
> > > 1DKE =--- 
> > >  14%
> > 
> > But (while Alphafold models are wonderful, have put us all out of jobs, 
> > etc, etc) they are just a starting point for my project and, for this 
> > purpose, no good in themselves.
> > 
> > Martin, Marcin - gemmi would be a good way to go, but - 
> > 
> > > >>> import gemmi
> > > >>> structure = gemmi.read_structure('old.pdb')
> > > >>> structure.make_mmcif_document().write_file('new.cif')
> > > 
> > > alphafill process new.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > > gemmi convert old.pdb gemmi.cif
> > > alphafill process gemmi.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > :-(
> > 
> > Arturo - I’ve never scripted PyMol, but saving as CIF from the graphics 
> > interface - 
> > 
> > > alphafill process pymol.cif filled.cif
> > > Structure file does not seem to contain polymers, perhaps 
> > > pdbx_poly_seq_scheme is missing?
> > 
> > 
> > Avinash - Maxit *might* work, but I fell at the first hurdle - although the 
> > help page says 
> > 
> > > Note: It is highly recommended to utilize binary distribution,
> > 
> > it’s not obvious where to get this. So I download and try to 

Re: [ccp4bb] CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324) (out of office)

[Elisabeth Laurent]

Thank you for your e-mail. I am out of office until January 2nd, 2024.
I will respond to your e-mail as soon as possible upon my return. 
For urgent matters please contact: b...@boku.ac.at
Thank you for your understanding.

With kind regards,
Elisabeth Laurent

>>> CCP4BB automatic digest system  23.12.23 01:00 >>>

There are 4 messages totaling 667 lines in this issue.

Topics of the day:

  1. Two-year postdoctoral position in time-resolved crystallography at IBS in
 Grenoble
  2. Postdoc opportunity at the PSI of Switzerland.
  3. Relion  issue with MPI
  4. Relion issue with MPI



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--

Date:Fri, 22 Dec 2023 10:20:57 +0100
From:Elke De Zitter 
Subject: Two-year postdoctoral position in time-resolved crystallography at IBS 
in Grenoble

Dear all, 

We have an immediate opening for a two-year postdoctoral researcher in SNaX 
team of the DYNAMOP group at the Institute for Structural Biology in Grenoble 
(France). The successful candidate will work on the development and 
optimization of bio-scavengers towards toxic organophosphorus compounds. To 
attain this goal, the researcher will use time-resolved crystallography and in 
silico protein design methods. The position is funded by the French National 
Research Agency via the University Grenoble Alpes, and is open for a young 
researcher. 

Applicants must have obtained a Ph.D. in structural biology, biochemistry, 
biophysics, physics, chemistry, or a related field, no more than two years 
before the start of the project. The candidate must show a track-record of 
publications in peer-reviewed journals, and is expected to be proficient in 
English and highly motivated to learn new skills. The candidate will work in 
the multidisciplinary DYNAMOP group and thus needs to be a good team player as 
well as being capable of working independently. While the research will be 
carried out in English, non-French-speaking candidates are expected to learn 
the basics of French in order to facilitate communication and integration into 
the laboratory. 
Experience with one or more of the following skills would be highly evaluated: 
protein design or the usage of artificial intelligence for structural biology, 
protein expression and purification, protein crystallization and macromolecular 
crystallography, serial crystallography, programming or scripting. 

Interested candidates can apply via [ 
https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996
 | 
https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996
 ] . We advice to contact Elke De Zitter (elke.de-zit...@ibs.fr) to obtain more 
information about the postdoctoral position and application procedure. 

All the best, 
Elke 

Elke De Zitter 
Institut de Biologie Structurale - IBS 
group DYNAMOP 
71 avenue des Martyrs 
38044 Grenoble Cedex 9, France 
+33 4 57 42 86 56 
elke.de-zit...@ibs.fr 



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--

Date:Fri, 22 Dec 2023 12:11:40 +
From:Panneels Valérie 
Subject: Postdoc opportunity at the PSI of Switzerland.


Dear Colleagues,

The Laboratory of Biomolecular Research at the Paul Scherrer Institute (PSI), 
Switzerland, is advertising for a Postdoc position from the NanoArgovia 
Programm of the Swiss Nanoscience Institute (SNI). This project is granted for 
one year and extendable to 2 years.

The project is based on Electron Diffraction Crystallography on proteins either 
photosensitive or involved in pharma applications. The PSI is the largest 
research institute for natural and engineering sciences in Switzerland 
(https://www.psi.ch/en) and hosts a synchrotron, the X-ray free electron laser 
SwissFEL and an electron microscopy facility (https://www.psi.ch/en/emf). The 
BIO division together with our PSI detector group has developed a unique 
instrument for electron diffraction with a dedicated ED-detector based on PSI 
detector technology.

Our laboratory (please consult https://www.psi.ch/en/lbr) is focused on 
studying the mechanism of action 

Re: [ccp4bb] [ccp4bb] Fragmented Chains after Automated Rebuilding

[Goldman, Adrian]

Surely in this day and age, one would just run AF2? - it’s clearly the best 
homology modelling program ever, finding homologies that other programs can’t 
reach.  I would - we are - using it to supply another “best guess” for 
difficult-to-build structures. One could even use it as an input for MR and 
hope.

Adrian

On 6 Oct 2022, at 17:24, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:

Dear Shawn,

I am not aware of an automated way to merge all fragments into a single 
consistent peptide chain. What I would do is to look at the map and the built 
fragments in coot and switch the symmetry on with a large radius, e.g. 20-30A 
and see if you can find a set of fragments (including symmetry mates) that 
could form a complete and consistent protein molecule.

If there is a suitable MR model available, I would try to match the fragments 
to the model (find equivalent amino acids). You could use the matching residues 
to superimpose the MR model e.g. onto the largest fragment available. The next 
step would be to rebuild the MR model using the electron density map and the 
built fragments as a guide.

If there is no suitable MR model, I would probably built the whole protein, 
starting from the largest fragment, using the built residues as a guide. For 
this you can use the “add residue” option and put the residue created at the 
position of the equivalent residue of a fragment. Every 3-5 residues, you 
should do a real space refinement. The pdb standard accepts negative residue 
numbers, so you should be able to build in N-terminal direction as well.  
Afterwards you will have to renumber the protein to get the correct numbering.

The alternative would be to select the correct symmetry mate for each fragment, 
write them out, renumber them and merge them into a single pdb file. However, 
in my experience, this is much more hassle than the build them “from scratch” 
as I mentioned.

Good luck,
Herman



Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Shawn Rumrill
Gesendet: Mittwoch, 5. Oktober 2022 22:42
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Fragmented Chains after Automated Rebuilding

Hello All,

I am trying to solve a protein/nucleic acid (na) structure. The density for na 
is poor and MR is less straightforward, so I used ModelCraft for automated 
phasing, rebuilding and improving the electron density. It has built a partial 
model for the complex, which looks somewhat reasonable, however, the protein 
and na chains are fragmented, which throws off numbering, etc. I'm sure this is 
expected, but I typically don't do automated rebuilding (necessary in this 
case).

Is there any way to easily connect and renumber the chains and residues 
(perhaps using a reference PDB structure) to try and build something more 
complete (in terms of chains and residues)?

I have not worked with a protein/na complex so certainly na modeling is new to 
me. Any input is greatly appreciated!

Thanks for your expertise,

Shawn



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Re: [ccp4bb] CCP4BB Digest - 30 Nov 2021 to 1 Dec 2021 (#2021-335)

[Crowley, Peter]

Subject: Re: High-order oligomers vs robust crystals - references?

Hi Frank et al.
Joining the discussion at this humorous stage...

What about Janin's contributions on crystal packing versus oligomer interfaces? 
There are useful ideas in this assessment:
https://www.cambridge.org/core/journals/quarterly-reviews-of-biophysics/article/abs/proteinprotein-interaction-and-quaternary-structure/670665304EE0AFE280652CCBBA3F55D1


Peter

_

Peter Crowley PhD
Professor (Protein Chemistry)

School of Chemistry
Orbsen Building
National University of Ireland, Galway
University Road
Galway
Ireland

Ph: + 353 91 49 24 80
http://www.nuigalway.ie/our-research/people/chemistry/petercrowley/

From: CCP4 bulletin board  on behalf of CCP4BB automatic 
digest system 
Sent: Thursday, December 2, 2021 12:00 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: CCP4BB Digest - 30 Nov 2021 to 1 Dec 2021 (#2021-335)

EXTERNAL EMAIL: This email originated from outside of NUI Galway. Do not open 
attachments or click on links in the message unless you recognise the sender's 
email address and believe the content is safe.
RÍOMHPHOST SEACHTRACH: Tháinig an ríomhphost seo as áit éigin taobh amuigh de 
OÉ Gaillimh. Ná cliceáil ar naisc agus ná hoscail ceangaltáin mura n-aithníonn 
tú seoladh ríomhphoist an tseoltóra agus mura gcreideann tú go bhfuil an 
t-ábhar sábháilte.


There are 5 messages totaling 677 lines in this issue.

Topics of the day:

  1. High-order oligomers vs robust crystals - references?
  2. Four open postdoc positions @ NIH
  3. JCSG structure validation server (3)



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--

Date:Wed, 1 Dec 2021 07:33:20 +
From:Frank von Delft 
Subject: Re: High-order oligomers vs robust crystals - references?

Dear all, thanks all for the several references you emailed around.

Here's a summary:

A Suite of Engineered GFP Molecules for Oligomeric Scaffolding
https://www.sciencedirect.com/science/article/pii/S0969212615002890

Dimerization properties of the RpBphP2 chromophore-binding domain
crystallized by homologue-directed mutagenesis
https://pubmed.ncbi.nlm.nih.gov/22868772/

An approach to crystallizing proteins by synthetic symmetrization
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1637565/

Why protein crystals favour some space-groups over others
https://www.nature.com/articles/nsb1295-1062

Infinite Assembly of Folded Proteins in Evolution, Disease,and Engineering
https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201806092



James Holton duly challenged me, and here's my reply:

JH: If I told you "no, that's not true", how would you go about
proving me wrong?  What would that data look like?
--
FvD: Geezus, I don't know!   It's not me that hurled this brainfart
around the grant funding agencies 20 years ago... That's why I asked
the Social Brain.

But my primary goal was to have something to stick into the
introduction to a paper, so that has been achieved. Whether it's
ethical to perpetuate a brainfart by citing other expressions of the
brainfart is a reasonable question, but this one would rank quite
low on the impact-of-transgression scale, methinks.


But Dhiraj's reply to my original question is a surely a better one:
/"Recently there were few articles where synthetic symmetrization was
used to enhance the crystallizability. proteins used were MBP, lysozyme
and GFP to name a few."//
/
It implies the weight-of-evidence is out there - hint to you
enterprising students, looking for something *actually useful* to write
a review about!

Frank



On 12/11/2021 14:52, Frank von Delft wrote:
> Hello all
>
> Two decades ago, I remember (!) much talk about a reason that
> bacterial proteins crystallize "more easily" is that they tend to come
> as oligomers (dimers and up), and that this internal symmetry made
> them happier to crystallize.
>
> Did anybody ever publish hard evidence?  Or even, is there a primary
> citation for the idea?
>
> Thanks
> Frank
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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> available at 

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Harry Powell - CCP4BB]

Hi Jon

Just checked an mmCIF file for one of the AlphaFold models - the model number 
is “1”, no sign of a model 0 that I can see…

A quick “sed” script could sort them all out…

Harry

> On 10 Nov 2021, at 12:22, Jon Agirre  wrote:
> 
> It might be, because the mmCIF versions work fine with MG.
> 
> On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> Hi folks
> 
> Been a while, but I’ve been doing some work on checking that some files are 
> valid PDB files and went back to the documentation; as far as I can work out, 
> the best solution to this is John Walker’s, because “MODEL 0” is not allowed 
> in the standard (maybe it is for mmCIF…) - 
> 
> > On 27 Aug 2021, at 16:39, John R. Walker  wrote:
> > 
> > I just change MODEL 0 to MODEL 1 then it works fine.
> > 
> > John
> 
> As far as I can see (from a small sample of the 150,000 AlphaFold models, 
> soon to be a few more...) all the PDB files downloadable from 
> alphafold.ebi.ac.uk are non-conformant. The documentation on PDB files that I 
> have been able to find easily says - 
> 
> > Details 
> > 
> > * This record is used only when more than one model appears in an entry. 
> > Generally, it is 
> > employed only for NMR structures. The chemical connectivity should be the 
> > same for each model. 
> > ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model 
> > structure are 
> > interspersed as needed between MODEL and ENDMDL records. 
> > 
> > * The numbering of models is sequential beginning with 1. 
> 
> Harry 
> 
> > 
> > On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE 
> >  wrote:
> > Dear Nick,
> > 
> >  
> > 
> > I had just looked at a pdb downloaded from the alphafold server without 
> > problems. However, then I realized that I had looked at the alphafold model 
> > after I had it superimposed on my own structure. Loading the alphafoldmodel 
> > directly in coot failed for me as well.
> > 
> >  
> > 
> > By looking into the pdb file, I discovered that the alphafold file has a 
> > “MODEL” record just before the coordinates and an “ENDMDL” record after the 
> > coordinates. After deleting these two records, the alphafold pdb loads fine.
> > 
> >  
> > 
> > Hope this helps,
> > 
> > Herman
> > 
> >  
> > 
> > Von: CCP4 bulletin board  Im Auftrag von Nicholas 
> > Keep
> > Gesendet: Freitag, 27. August 2021 16:51
> > An: CCP4BB@JISCMAIL.AC.UK
> > Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 
> > 
> >  
> > 
> > Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half 
> > dozen or so I have tried to read into CCP4mg or coot the PDB has always 
> > failed but the CIF is fine.  I can then write out a PDB if I want.
> > 
> > I could add to the conspiracy theories that this is EBI trying to 
> > normalise use of CIF format, but I suspect it is something much more 
> > mundane, that should be addressed.
> > 
> > Best wishes
> > 
> > Nick
> > 
> > -- 
> > NOTE NEW PHONE NUMBER JULY 2020
> > 
> > I do not work Mondays. For urgent business on a Monday contact Clare 
> > Woodward (Director of Operations) or Gillian Forrester (Deputy Dean)
> > 
> > Prof Nicholas H. Keep
> > Executive Dean of School of Science
> > Professor of Biomolecular Science
> > Crystallography, Institute for Structural and Molecular Biology,
> > Department of Biological Sciences
> > Birkbeck, University of London,
> > Malet Street,
> > Bloomsbury
> > LONDON
> > WC1E 7HX
> > 
> > Office G54a
> > 
> > Dean Email; scid...@bbk.ac.uk
> > Dept email n.k...@mail.cryst.bbk.ac.uk
> > Telephone 020-3926-3475 (Will contact me at home if working as well as my 
> > office)
> > 
> > If you want to access me in person you have to come to the crystallography 
> > entrance
> > and ring me or the department office from the internal phone by the door
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > 
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> > list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> > https://www.jiscmail.ac.uk/policyandsecurity/
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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> 
> 
> -- 
> 

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Jon Agirre]

It might be, because the mmCIF versions work fine with MG.

On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi folks
>
> Been a while, but I’ve been doing some work on checking that some files
> are valid PDB files and went back to the documentation; as far as I can
> work out, the best solution to this is John Walker’s, because “MODEL 0” is
> not allowed in the standard (maybe it is for mmCIF…) -
>
> > On 27 Aug 2021, at 16:39, John R. Walker 
> wrote:
> >
> > I just change MODEL 0 to MODEL 1 then it works fine.
> >
> > John
>
> As far as I can see (from a small sample of the 150,000 AlphaFold models,
> soon to be a few more...) all the PDB files downloadable from
> alphafold.ebi.ac.uk are non-conformant. The documentation on PDB files
> that I have been able to find easily says -
>
> > Details
> >
> > * This record is used only when more than one model appears in an entry.
> Generally, it is
> > employed only for NMR structures. The chemical connectivity should be
> the same for each model.
> > ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model
> structure are
> > interspersed as needed between MODEL and ENDMDL records.
> >
> > * The numbering of models is sequential beginning with 1.
>
> Harry
>
> >
> > On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE <
> herman.schreu...@sanofi.com> wrote:
> > Dear Nick,
> >
> >
> >
> > I had just looked at a pdb downloaded from the alphafold server without
> problems. However, then I realized that I had looked at the alphafold model
> after I had it superimposed on my own structure. Loading the alphafoldmodel
> directly in coot failed for me as well.
> >
> >
> >
> > By looking into the pdb file, I discovered that the alphafold file has a
> “MODEL” record just before the coordinates and an “ENDMDL” record after the
> coordinates. After deleting these two records, the alphafold pdb loads fine.
> >
> >
> >
> > Hope this helps,
> >
> > Herman
> >
> >
> >
> > Von: CCP4 bulletin board  Im Auftrag von
> Nicholas Keep
> > Gesendet: Freitag, 27. August 2021 16:51
> > An: CCP4BB@JISCMAIL.AC.UK
> > Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 
> >
> >
> >
> > Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half
> > dozen or so I have tried to read into CCP4mg or coot the PDB has always
> > failed but the CIF is fine.  I can then write out a PDB if I want.
> >
> > I could add to the conspiracy theories that this is EBI trying to
> > normalise use of CIF format, but I suspect it is something much more
> > mundane, that should be addressed.
> >
> > Best wishes
> >
> > Nick
> >
> > --
> > NOTE NEW PHONE NUMBER JULY 2020
> >
> > I do not work Mondays. For urgent business on a Monday contact Clare
> Woodward (Director of Operations) or Gillian Forrester (Deputy Dean)
> >
> > Prof Nicholas H. Keep
> > Executive Dean of School of Science
> > Professor of Biomolecular Science
> > Crystallography, Institute for Structural and Molecular Biology,
> > Department of Biological Sciences
> > Birkbeck, University of London,
> > Malet Street,
> > Bloomsbury
> > LONDON
> > WC1E 7HX
> >
> > Office G54a
> >
> > Dean Email; scid...@bbk.ac.uk
> > Dept email n.k...@mail.cryst.bbk.ac.uk
> > Telephone 020-3926-3475 (Will contact me at home if working as well as
> my office)
> >
> > If you want to access me in person you have to come to the
> crystallography entrance
> > and ring me or the department office from the internal phone by the door
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
>
> 
>
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>
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>


-- 
Dr Jon Agirre
Royal Society Olga Kennard Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

[Harry Powell - CCP4BB]

Hi folks

Been a while, but I’ve been doing some work on checking that some files are 
valid PDB files and went back to the documentation; as far as I can work out, 
the best solution to this is John Walker’s, because “MODEL 0” is not allowed in 
the standard (maybe it is for mmCIF…) - 

> On 27 Aug 2021, at 16:39, John R. Walker  wrote:
> 
> I just change MODEL 0 to MODEL 1 then it works fine.
> 
> John

As far as I can see (from a small sample of the 150,000 AlphaFold models, soon 
to be a few more...) all the PDB files downloadable from alphafold.ebi.ac.uk 
are non-conformant. The documentation on PDB files that I have been able to 
find easily says - 

> Details 
> 
> * This record is used only when more than one model appears in an entry. 
> Generally, it is 
> employed only for NMR structures. The chemical connectivity should be the 
> same for each model. 
> ATOM, HETATM, SIGATM, SIGUIJ, ANISOU, and TER records for each model 
> structure are 
> interspersed as needed between MODEL and ENDMDL records. 
> 
> * The numbering of models is sequential beginning with 1. 

Harry 

> 
> On Fri, Aug 27, 2021 at 11:03 AM Schreuder, Herman /DE 
>  wrote:
> Dear Nick,
> 
>  
> 
> I had just looked at a pdb downloaded from the alphafold server without 
> problems. However, then I realized that I had looked at the alphafold model 
> after I had it superimposed on my own structure. Loading the alphafoldmodel 
> directly in coot failed for me as well.
> 
>  
> 
> By looking into the pdb file, I discovered that the alphafold file has a 
> “MODEL” record just before the coordinates and an “ENDMDL” record after the 
> coordinates. After deleting these two records, the alphafold pdb loads fine.
> 
>  
> 
> Hope this helps,
> 
> Herman
> 
>  
> 
> Von: CCP4 bulletin board  Im Auftrag von Nicholas Keep
> Gesendet: Freitag, 27. August 2021 16:51
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] A "funny" thing related to AlphaFold2 
> 
>  
> 
> Has anyone made use of an Alpha Fold PDB as opposed to CIF.  On the half 
> dozen or so I have tried to read into CCP4mg or coot the PDB has always 
> failed but the CIF is fine.  I can then write out a PDB if I want.
> 
> I could add to the conspiracy theories that this is EBI trying to 
> normalise use of CIF format, but I suspect it is something much more 
> mundane, that should be addressed.
> 
> Best wishes
> 
> Nick
> 
> -- 
> NOTE NEW PHONE NUMBER JULY 2020
> 
> I do not work Mondays. For urgent business on a Monday contact Clare Woodward 
> (Director of Operations) or Gillian Forrester (Deputy Dean)
> 
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck, University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
> 
> Office G54a
> 
> Dean Email; scid...@bbk.ac.uk
> Dept email n.k...@mail.cryst.bbk.ac.uk
> Telephone 020-3926-3475 (Will contact me at home if working as well as my 
> office)
> 
> If you want to access me in person you have to come to the crystallography 
> entrance
> and ring me or the department office from the internal phone by the door
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] CCP4BB Digest - 14 Sep 2021 to 15 Sep 2021 - Special issue (#2021-265)

[Jacqui Gulbis]

Hi Aaron, thank you for your tribute to an extraordinary scientist; It brought 
back happy memories.

Jack Dunitz visited Australia in the late ‘80s,  possibly for the IUCr meeting 
in Perth, and I can recall his razor wit and much hilarity when he, Sandy 
Mathieson, and Jim Morrison were recalling their early days in science.

Vale Jack.


From: CCP4 bulletin board  on behalf of CCP4BB automatic 
digest system 
Date: Thursday, 16 September 2021 at 02:15
To: CCP4BB@JISCMAIL.AC.UK 
Subject: CCP4BB Digest - 14 Sep 2021 to 15 Sep 2021 - Special issue (#2021-265)
There are 9 messages totaling 130442 lines in this issue.

Topics in this special issue:

  1. Prof. Jack Dunitz, 1923-2021
  2. software DS, fconv still available ? contact?
  3. Call for EMBL Hamburg Synchrotron Beamtime Applications
  4. Phosphatase enzymatic assay (3)
  5. AW: Phosphatase enzymatic assay
  6. MX-RDR - Macromolecular Xtallography Raw Data Repository
  7. Postdoctoral Research Opportunity in Cryo-EM at University of Washington,
 in Seattle, USA



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--

Date:Tue, 14 Sep 2021 22:18:48 -0700
From:Robert Stroud 
Subject: Re: Prof. Jack Dunitz, 1923-2021

Thanks Aaron, a beautiful recognition of a great scientist.

Robert Stroud
str...@msg.ucsf.edu



> On Sep 14, 2021, at 10:13 AM, Aaron Finke  wrote:
>
> Dear all,
>
> It is with a heavy heart that I announce the passing of Prof. Jack Dunitz at 
> the age of 98. Prof. Dunitz was a giant in the development of modern 
> crystallographic methods, most notably in the determination of the crystal 
> structure of ferrocene, confirming the “sandwich complex” nature of that 
> molecule and ushering in the field of organometallic chemistry. As a 
> crystallographer, mathematician, and chemist, Prof. Dunitz effectively 
> bridged the gap between crystallography and chemistry, inspiring chemists to 
> exploit the utility of the burgeoning field of crystallography. He was a 
> professor at ETH-Zurich for over 60 years, and even after his “retirement” in 
> 1990, dedicated his life to crystallographic research.
>
> I have many fond memories of Prof. Dunitz from my time at ETH. Even at the 
> age of 91, he still came into the office at least three times a week to 
> pursue research programs; I am told he continued to come in regularly until 
> Covid forced the campus closed. His wit and curiosity never dulled, and was 
> enamored with new technologies that enabled various new forms of 
> crystallographic research. He owned an iPad before I ever did! As a postdoc 
> doing crystallography, Prof. Dunitz enjoyed calling me into his office, 
> ostensibly to help him use some feature of CCDC Mercury, but in reality to 
> discuss some new idea he had about crystal symmetry and exploiting it to gain 
> some greater understanding of coordination complexes. He was the kind of 
> person who had forgotten more chemistry than I will ever know, and these 
> discussions were always enlightening and entertaining, mixing new theory with 
> the history of crystallography, much of which he bore witness or contributed 
> to. He will be sorely missed.
>
> If you would like to express your condolences, please use the following email 
> address:  jack_condole...@ethz.ch 
>
> Aaron
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu 
>
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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--

Date:Wed, 15 Sep 2021 09:25:48 +0200
From:Guenter Fritz 
Subject: Re: software DS, fconv still available ? contact?

Dear Manfred,

thanks a lot. I had checked the homepage before. There is a note that
the software is not any more available  for download from their site.
But no further hint whether it is available somewhere else.

Best regards,

Re: [ccp4bb] [ccp4bb] AW: [ccp4bb] (R)MS

[Randy John Read]

It’s also important to keep in mind that, in this equation, u is the component 
of the displacement *in the direction of the diffraction vector*.  If you 
assume isotropic displacements and you know the mean-squared value of the 
overall xyz vector displacement, you have to divide that mean-squared value by 
3 to get the variance in any particular direction.  This is a source of 
considerable confusion in crystallography textbooks!

Best wishes,

Randy Read

> On 28 May 2021, at 11:09, Ian Tickle  wrote:
> 
> 
> Hi Jonathan
> 
> On Thu, 27 May 2021 at 18:34, Hughes, Jonathan 
>  wrote:
> 
>  "B = 8π2  where u is the r.m.s. displacement of a scattering center, and 
> <...> denotes time averaging"
> 
> Neither of those statements is necessarily correct: u is the _instantaneous_ 
> displacement which of course is constantly changing (on a timescale of the 
> order of femtoseconds) and cannot be measured.  So u2 is the squared 
> instantaneous displacement,   is the mean-squared displacement, and so 
> the root-mean-squared displacement (which of course is amenable to 
> measurement) is sqrt(), not the same thing at all as u.
> 
> Incidentally, the 8π2 constant factor comes from Fourier-transforming the 
> Debye-Waller factor expression I mentioned earlier.
> 
> Also for crystals at least, the averaging is not only over time, it's over 
> all unit cells, i.e. the displacements are not only thermal in origin but 
> also due to spatial static disorder (instantaneous differences between unit 
> cells).
> 
> it would seem to me that we would be able to interpret things MUCH more 
> easily with u rather than anything derived from u².
> 
> So then I think what you mean is sqrt() rather than , which seems not 
> unreasonable.
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
>  
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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Re: [ccp4bb] CCP4BB Digest - 25 May 2021 to 26 May 2021 (#2021-147)

[James Krieger]

For the NMR structure ensemble, you could calculate root mean square 
fluctuations (RMSFs) and put them into the B factor column. This is a fairly 
common analysis within molecular dynamics software. You could also use the 
ProDy Python API to do this.

ProDy also has command line apps including one for writing out biomol 
assemblies, which could be added to the growing list too.

Best wishes 
James 

> On May 27, 2021, at 00:03, CCP4BB automatic digest system 
>  wrote:
> 
> There are 40 messages totaling 21155 lines in this issue.
> 
> Topics of the day:
> 
>  1. writing coordinates of full biomol into one (PDB) file (4)
>  2. Postdoctoral position in structural biology of comammox in Vienna
>  3. PhD position, University of Konstanz
>  4. Fwd: Abstract submission deadline extended to 2 June - PSB Symposium
> "Frontiers in Bioimaging", 1-2 July 2021
>  5. Unmodeled density (12)
>  6. External: Re: [ccp4bb] Unmodeled density
>  7. Analysis of NMR ensembles (19)
>  8. Fully-funded PhD at the University of Liverpool
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
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> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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> 
> --
> 
> Date:Tue, 25 May 2021 16:58:49 -0700
> From:Pavel Afonine 
> Subject: Re: writing coordinates of full biomol into one (PDB) file
> 
> Hi Frank,
> 
> phenix.pdb.biomt_reconstruction command should do it.
> 
> Pavel
> 
>> On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
>> frank.vonde...@cmd.ox.ac.uk> wrote:
>> 
>> Hello all - this presumably has a really simple solution:
>> 
>> For a PDB file with a (correct) biomolecular assembly record (REMARK
>> 350), what program do I use to generate and write out the coordinates of
>> the biomolecular assembly (or one of them).
>> 
>> Thanks
>> Frank
>> 
>> 
>> 
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>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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> 
> --
> 
> Date:Wed, 26 May 2021 07:05:26 +0200
> From:Kristina Djinovic Carugo 
> Subject: Postdoctoral position in structural biology of comammox in Vienna
> 
> *Postdoctoral position in structural biology of comammox in Vienna*
> 
> For 120 years, microbiologists had strongly assumed that nitrification 
> must be performed by two distinct groups of microorganisms 
> (‘nitrifiers’) in cooperation: the ammonia oxidizers and the nitrite 
> oxidizers, respectively. This scientific dogma broke in 2016, when 
> ‘complete ammonia oxidizers’ were discovered (1). In collaboration with 
> the research lab (Daims/Wagner) who discovered the comammox bacterium 
> Djinovic lab plans to structurally and biochemically characterize 
> selected enzymes of the comammox, with the aim to decipher the catalytic 
> mechanism and to identify those structural determinants of the substrate 
> affinity and specificity.
> 
> *Qualifications and experience: *The applicants should hold a recent PhD 
> degree in a relevant field with a structural biology experience. Strong 
> background in molecular cloning, expression, and purification of protein 
> complexes is essential. Prior knowledge of crystallography and/or 
> single-particle electron microscopy is needed. Excellent spoken and 
> written English are required.
> 
> Applications are accepted through *Vienna International Postdoctoral 
> Program (VIP^2 )*, details on the program which offers excellent 
> research environment,tructured training and career development program 
> are available here:
> 
> https://training.vbc.ac.at/post-docs/vip2-post-doc-program/ 
> 
> 
> *Deadline*: 15^th June 2021
> 
> For details in the project contact please contact: Kristina Djinovic 
> Carugo kristina.djino...@univie.ac.at 
> 
> 
> 1.Daims, H., Lebedeva, E. V., Pjevac, P., Han, P., Herbold, C., 
> Albertsen, M., Jehmlich, N., Palatinszky, 

Re: [ccp4bb] CCP4BB Digest - 13 Feb 2021 to 14 Feb 2021 (#2021-51)

[Eric Pettersen]

> On Feb 14, 2021, at 4:00 PM, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Sat, 13 Feb 2021 20:24:07 -0500
> From:Nicholas Larsen  >
> Subject: Re: Bug in mmCIF handling of UNK residues?
> 
> I hope this doesn't confuse the discussion, but my understanding was "UNK"
> stood for "unknown" residue and this will cause errors.  UNK naming
> convention is the default output of Schrodinger when generating ligand PDB
> files.  Coot will display the PDB containing "UNK" as a residue, but if you
> try to use the CIF file to real-space refine, the ligand will blow up.   I
> found that renaming the residue in the output PDB and regenerating the CIF
> file with the corrected RESID name solved the problem.  So in
> my experience, the problem is the name "UNK" and this just needs to be
> switched to something else.  Has anyone else seen this?
> Nick

The PDB defines UNK as unknown amino acid.  UNL is unknown ligand.  N is 
unknown nucleic acid.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab





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[ccp4bb] ccp4bb PhD position oppurtunity

[Thatipally Mounika]

Dear Dr Xinlai Cheng,

My name is Mounika, have completed Masters in Biotechnology in the 2019
from Hyderabad India. I am writing this mail regarding any PhD positions
offered in your lab. I feel that pursuing PhD in onco biology would help me
reach my dream and also be among one who could try giving a solution to
cancer. I have read that your research interest area is also cancer
therapy. I have also read your article on the anti-tumor properties of gold
which made me think about the various ways to address cancer. I would love
to start working on a project in your lab, if possible. The below attached
is my resume and a scientific write up. I look forward to hear from you.

Thanking you,

Mounika Thatipally.

  mounika resume-pdf.pdf


  Standard operating procedure- pdf.pdf




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Re: [ccp4bb] CCP4BB Digest - 29 Dec 2020 to 30 Dec 2020 (#2020-345)

[s.j.smer...@bham.ac.uk]

Hi Anamika,

Just to be clear, the M13 ori is for production of ssDNA using a helper phage. 
Replication of that plasmid is more likely from another ColE1-derived origin 
elsewhere on the vector and also likely to give high copy numbers - which it 
seems it does. The p15 ori is indeed quite a low copy number origin, around 
10-20 copies per cell as I remember but you can look that up. I would suggest 
trying a PCR using vector- and insert-specific primers as a diagnostic in the 
first instance and work from there.

Best

Steve

***

Steve Smerdon
Professor of Structural Biology
Institute of Cancer and Genomic Sciences
1st Floor IBR West (WX 1.19)
University of Birmingham,
Vincent Drive, Edgbaston,Birmingham,
B15 2TT
UNITED KINGDOM.
Office: +44(0)121 414 9241
Mobile: +44(0)7887852951

***
 

On 31/12/2020, 00:03, "CCP4 bulletin board on behalf of CCP4BB automatic 
digest system"  
wrote:

There is 1 message totaling 88 lines in this issue.

Topics of the day:

  1. OFFTOPIC question "Two plasmids in one host cell"



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--

Date:Wed, 30 Dec 2020 11:35:24 +0200
From:Anamika Singh 
Subject: OFFTOPIC question "Two plasmids in one host cell"

Hi All,

I have two constructs having different ori, p15ori and M13 ori, different
promoters araBAD promoter and LacI, and different antibiotic resistance
chloramphenicol and Ampicillin respectively.
I am managed to get the transformants and getting the expected result after
blunt digestion with the EcoRV enzyme. Since both the plasmids have the
site for EcoRV. But the p15 ori has a low copy number that's why I am
seeing the very faint band as compared to other plasmid in the sample.

So I would like to know is there any way that I can quantify the low copy
number plasmid.
Because I am not able to sequence it with the specific primers it could be
due to its low concentration.

Please advise.

Thank you.
-- 
Dr. Anamika Singh
Post-Doctoral Fellow
Silberman Institute of Life Sciences
Hebrew University of Jerusalem, Israel
No: 054-294-8036



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End of CCP4BB Digest - 29 Dec 2020 to 30 Dec 2020 (#2020-345)
*





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Re: [ccp4bb] [ccp4bb] Up-to-date 3D stereo solution

[Phoebe A. Rice]

Ah yes, fond memories of that mirrored contraption!  
There were also wooden contraptions to strap on one's head with image-merging 
mirrors in them.  We had fun lining up equal-height friends and merging them. 
But both of those did have the downside that getting engrossed in electron 
density while keeping one's head properly positioned caused back issues even in 
my student days.  

On 12/13/20, 6:38 AM, "CCP4 bulletin board on behalf of Goldman, Adrian" 
 wrote:

the “best” I’ve found is stereo glasses and display side-by-side stereo. 

When I was a graduate student in the Steitz lab a WHILE ago, there was a 
frame built that fit over the Evans and Sutherland Ps2 and PS390 monitors (I 
said a while ago :)) that carried two mirrors at 45 degrees at your eye width 
apart, and another two at 45 degrees towards the edge of the screen.The 
whole device was counterweighted and could be lowered into place or pulled up 
for non-stereo work.  You put your nose on the centre of the two mirrors.

For side by side stereo, it can’t be beat.  Immersive, no eye-strain.  I 
have debated having something similar made…

Adrian

> On 12 Dec 2020, at 17:07, Hughes, Jonathan 
 wrote:
> 
> just cross your eyes.
> jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board  Im Auftrag von Jan 
Stransky
> Gesendet: Samstag, 12. Dezember 2020 12:11
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] Up-to-date 3D stereo solution
> 
> Dear all,
> 
> I am wondering, if anyone has experience with implementing stereo 3D 
setup with currently available hardware. NVIDIA 3D vision seems to be pretty 
much dead.
> 
> The primary usage would be model building in Coot, but also potentially 
Pymol analysis.
> 
> The biggest issue is an access to controls. We played a bit with PS VR, 
VR solutions prsented last year at CCP4 weekend seem to be still far from 
usable.
> 
> Did anyone try AR?
> 
> Best regards,
> 
> Jan
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
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> 
> 
> 
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Re: [ccp4bb] [ccp4bb] Up-to-date 3D stereo solution

[Goldman, Adrian]

the “best” I’ve found is stereo glasses and display side-by-side stereo. 

When I was a graduate student in the Steitz lab a WHILE ago, there was a frame 
built that fit over the Evans and Sutherland Ps2 and PS390 monitors (I said a 
while ago :)) that carried two mirrors at 45 degrees at your eye width apart, 
and another two at 45 degrees towards the edge of the screen.The whole 
device was counterweighted and could be lowered into place or pulled up for 
non-stereo work.  You put your nose on the centre of the two mirrors.

For side by side stereo, it can’t be beat.  Immersive, no eye-strain.  I have 
debated having something similar made…

Adrian

> On 12 Dec 2020, at 17:07, Hughes, Jonathan 
>  wrote:
> 
> just cross your eyes.
> jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board  Im Auftrag von Jan Stransky
> Gesendet: Samstag, 12. Dezember 2020 12:11
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] Up-to-date 3D stereo solution
> 
> Dear all,
> 
> I am wondering, if anyone has experience with implementing stereo 3D setup 
> with currently available hardware. NVIDIA 3D vision seems to be pretty much 
> dead.
> 
> The primary usage would be model building in Coot, but also potentially Pymol 
> analysis.
> 
> The biggest issue is an access to controls. We played a bit with PS VR, VR 
> solutions prsented last year at CCP4 weekend seem to be still far from usable.
> 
> Did anyone try AR?
> 
> Best regards,
> 
> Jan
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
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> 
> 
> 
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Re: [ccp4bb] [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Randy John Read]

Several people have mentioned lack of peer review as a reason to doubt the 
significance of the AlphaFold2 results.  There are different routes to peer 
review and, while the results have not been published in a peer review journal, 
I would have to say (as someone who has been an assessor for two CASPs, as well 
as having editorial responsibilities for a peer-reviewed journal), the peer 
review at CASP is much more rigorous than the peer review that most papers 
undergo.  The targets are selected from structures that have recently been 
solved but not published or disseminated, and even just tweeting a C-alpha 
trace is probably enough to get a target cancelled.  In some cases (as we’ve 
heard here) the people determining the structure are overly optimistic about 
when their structure solution will be finished, so even they may not know the 
structure at the time it is predicted.  The assessors are blinded to the 
identities of the predictors, and they carry out months of calculations and 
inspections of the models, computing ranking scores before they find out who 
made the predictions.  Most assessors try to bring something new to the 
assessment, because the criteria should get more stringent as the predictions 
get better, and they have new ideas of what to look for, but there’s always 
some overlap with “traditional” measures such as GDT-TS, GDT-HA (more stringent 
high-accuracy version of GDT) and lDDT.

Of course we’d all like to know the details of how AlphaFold2 works, and the 
DeepMind people could have been (and should be) much more forthcoming, but 
their results are real.  They didn’t have any way of cheating, being selective 
about what they reported, or gaming the system in any other way that the other 
groups couldn’t do.  (And yes, when we learned that DeepMind was behind the 
exceptionally good results two years ago at CASP13, we made the same half-jokes 
about whether Gmail had been in the database they were mining!)

Best wishes,

Randy Read

> On 9 Dec 2020, at 10:36, Hughes, Jonathan 
>  wrote:
> 
> i think the answer to all these doubts and questions is quite simple: the 
> AlphaFold2 people must make all details of their methods public (source code) 
> and, as would probably be necessary, open their system for inspection and use 
> by independent experts. isn't that what peer review and reproducibility are 
> all about? those rules date from the time before every tom, dick and 
> henriette could publicize anything they like inside their own zuckerberg 
> bubble. my opinion is that this is a virtual infectious disease that will 
> cause humanity far bigger problems than corona ever will – i just hope i'm 
> wrong!
> best
> jon
>  
> Von: CCP4 bulletin board  Im Auftrag von Mark J van 
> Raaij
> Gesendet: Mittwoch, 9. Dezember 2020 11:14
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and 
> less pipetting (?)
>  
> on the day the news came out, I did wonder if the AlphaFold2 team somehow had 
> access to all the preliminary PDB files sent around via Gmail (which belongs 
> to the same company), but more as a joke/conspirational thought.
> "our" target T1052, was also predicted very well by domains and as a monomer. 
> It will be interesting to see how well future iterations of the method can 
> assemble the complete protein chain and the complete protein chains into the 
> correct heteromer.
>  
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> Section Editor Acta Crystallographica F
> https://journals.iucr.org/f/
> 
>  
> On 9 Dec 2020, at 10:37, Cedric Govaerts  wrote:
>  
> Dear All
>  
> After about 10 (!) years of (very) hard work we solved the structures of our 
> dearest membrane transporter.  Dataset at 2.9 And resolution, fairly 
> anisotropic, experimental phasing, and many long nights with Coot and 
> Buster to achieve model refinement. 
>  
> The experimental structure had a well defined ligand nicely coordinated but 
> also a lipid embedded inside the binding cavity (a complete surprise but 
> biologically relevant) and two detergent molecules well defined 
> (experimental/crystallisation artefact).
>  
> As our paper was accepted basically when CASP organisers were calling for 
> targets I offered my baby to the computing Gods. However we only provided the 
> sequence to CASP, no info regarding any ligand or lipid.
>  
> Less than a month after, the CASP team contacted us and send us the best 
> model.  In fact it was 2 half models as the transporter is a pseudo dimer, 
> with the N-lobe and C-lobe moving relative to each other during transport 
> cycle, thus divided as two domains in CASP.
>  
> The results were breathtaking. 0.7 And RSMD on one half, 0.6 on the other. 
> And yes, group 427 was the superpower (did not know at the time that it was 
> AlphaFold).
>  
> We had long discussions with 

Re: [ccp4bb] CCP4BB Digest - 28 May 2020 to 29 May 2020 (#2020-148)

[Jacqui Gulbis]

Ta

Now dear
My deadline for this grant is on the second
I will try to get a rewritten simplified version to you before tomorrow morning.
When I do PLEASE look it over and see if you can write in anything else wrt 
modelling - at present its not written in year 1
Also general check and approval
Thanks kid
jacq

On 30/5/20, 09:06, "CCP4 bulletin board on behalf of CCP4BB automatic digest 
system"  wrote:

There are 10 messages totaling 2125 lines in this issue.

Topics of the day:

  1. visual mask editor - why (2)
  2. Strange Pseudosymmetry Effects (2)
  3. Fwd: Refmac error (2)
  4. Job Offer at INNOVATION CAMPUS BERLIN in Computational Chemistry
  5. PDB file header lines... (3)



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Date:Fri, 29 May 2020 00:02:11 -0700
From:Pavel Afonine 
Subject: Re: visual mask editor - why

Hi Bernhard,

"Like comparing these map regions, excluding

intrusion of a solvent mask, etc.":

You didn't say much about the context.. So I'd say Polder map approach
comes to mind first based on these keywords. Next is "map comparison" (
https://doi.org/10.1107/S1399004714016289).

If none of the above: what we (or you) are missing?

Pavel

On Thu, May 28, 2020 at 11:17 AM Bernhard Rupp 
wrote:

> Maybe I should explain an example: Say coot detects an unmodelled blob
> (maybe a ligand). Now, I would like to do
>
> a number of things without biasing towards a model. Like comparing these
> map regions, excluding
>
> intrusion of a solvent mask, etc.
>
>
>
> Now could coot for example just generate a mask around what it already
> knows are blobs?
>
> Possible useful items could be a solvent mask not including that regions,
> or a density map
>
> that includes only features with a certain boundary around that blob.
>
>
>
> I pilfered some kludges together from different sources, but let’s just
> say inelegant would be a compliment.
>
>
>
> Best, BR
>
> 
>
> Brief question: Does something like a visual density mask editor exist?
>
> Thx, BR
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Date:Fri, 29 May 2020 09:34:23 +0100
From:Harry Powell - CCP4BB 
Subject: Re: Strange Pseudosymmetry Effects

Hi Tim

You could send out an SOS to some of the other authors in the same issue, 
who might have kept a copy - several are “regular" posters on this forum, e.g.

Sacha Urzhumtsev
Gerard Kleywegt
Eleanor Dodson

There’s a good chance they’ll be stuck at home at the moment with plenty of 
time to search through old boxes…

Harry

> On 28 May 2020, at 21:04, Tim Gruene  wrote:
> Dear Eddie, dear all
>
> According to ftp://ftp.ccp4.ac.uk/ccp4/newsletter/jun_95/, this article
> appeare in Newsletter June 95. It is mentioned in the table of contents,
> "Correction on perfection: primary extinction correction in protein
> crystallography" by Polykarpov and Sawyer.
> Unfortunately, the article itself is not there
>
> Extinction is not the same as the dynamic effects that James mentioned,
> but this seems the closest match.
>
> Would anyone have a copy they can share with me?
>
> Thanks a lot!
>
> Best,
>
> Tim



To 

Re: [ccp4bb] CCP4BB vs COVID19

[Jonathan Cooper]

 A bit off-topic, and not wishing to tempt fate, of course, here are the No. 
cases by date for two typical outer-London boroughs (of absolutely no 
particular interest to me ;-), one about 4 times bigger than the other: 
http://u.cubeupload.com/jbcooper/2020032316h22m13s.png
Could I be forgiven for seeing a bit of a plateau there? I saw an article 
yesterday saying you could only make the global numbers slope-off by taking 
logs on the Y-axis - the age-old adage that logs will flatten everything!! I 
haven't had to do that in this case. I'll be more crystallographic next time. 
On Sunday, 22 March 2020, 20:26:51 GMT, Darren Hart  
wrote:  
 
  Structure of 2019-nCov RNA polymerase:
 
https://www.biorxiv.org/content/10.1101/2020.03.16.993386v1.full.pdf+html
 
 Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex 
with cofactors nsp7 and nsp8 at a resolution of 2.9-Å...A comparative analysis 
to show how remdesivir binds to this polymerase is also provided. 
 
 Darren
 
 
 
 On 22/03/2020 19:18, Nikolay Dobrev wrote:
  
 
Dear all, I assume most of you are aware of the EMBL-EBI datahub which was set 
up in January to provide essential virus research data to all scientists, but 
in case someone missed it I would like to share the link: 
https://www.ebi.ac.uk/ena/pathogens/covid-19 
  You can find all relevant data, from COVID-19 genome sequencing data up to 
x-ray and cryo-EM structures of relevant proteins. 
  Stay healthy, Nikolay 
Nikolay Dobrev 
 Scientific Officer, Protein Expression and Purification Core Facility
 EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
 T +49 6221 387 8633 | M +49 173 684 0532
 twitter.com/EMBLorg | facebook.com/embl.org | youtube.com/user/emblmedia
 Visit www.embl.org/events for a complete list of all EMBL events.
 
  
   
  
   
 
 On Sun, Mar 22, 2020 at 17:26, DUMAS Philippe (IGBMC) 
 wrote: 
Relevant to the discussion: 
   * Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press 
An RNA Thermosensor Controls Expression of Virulence Genes in Listeria 
monocytogenes 
   * Bacterial RNA thermometers: molecular zippers and switches Jens Kortmann 
and Franz Narberhaus NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255
  
   *An RNA Thermometer Activity of the West Nile Virus Genomic 30-Terminal 
Stem-Loop Element Modulates Viral Replication Eciency during Host Switching 
Viruses 2020, 12, 104; doi:10.3390/v12010104
  
  * Temperature triggers immune evasion by Neisseria meningitidis  Edmund 
Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget Gollan2, 
Helen Ewles2, Ronald Chalmers3, Vladimir Pelicic2 & Christoph M. Tang1,2 Nature 
(2013) 
  Philippe Dumas  De: "James Holton" 
 À: "CCP4BB" 
 Envoyé: Dimanche 22 Mars 2020 16:38:28
 Objet: Re: [ccp4bb] CCP4BB vs COVID19
  
  Thank you Patrick,
 
 RNA structure is still structural biology, so I think relevant here.  It seems 
to me that RNA as a thermometer would be an easy hypothesis to test?  Has 
anyone measured virulence vs temperature in cell culture?  
 
 The 3D structure of the genome is no doublt important.  I wouldn't want to try 
crystallizing the whole thing, but I wonder if this might be an excellent 
target for cryoEM?  A challenge for that "we can classify our way out of 
anything" philosophy?  And the result would most certainly be interesting.
 
 -James Holton
 MAD Scientist
 
 On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote:
  
  
  James, this isn't conventional structural biology, but may be of interest, 
and I haven't been able get any mainstream virologists to think about it. 
  The protein sequences are obviously of interest, but so are the RNA sequences 
at both ends of the Covid genome, which have conserved secondary structure.  A 
few years ago a paper came out suggesting that wild-type influenza has multiple 
"RNA thermometers", which may play an important role in the tropism of 
influenza.  Similar mechanisms may exist in other respiratory viruses, 
including Covid. 
  My take on this, and the relevant papers, are below. 
  Good luck to everyone and stay well,  
  Patrick 
  
   
  
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
     
My paper in Medical Hypotheses 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf     
Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA 
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.     
Chursov, Andrey, et al. "Specific temperature-induced perturbations of 
secondary mRNA structures are associated with the cold-adapted 
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 
1266-1274.     
Yang, Dong, and Julian L. Leibowitz. "The structure and functions of 
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.       
 
  
  On Fri, Mar 20, 2020 at 10:59 PM James 

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Gihan Ketawala]

Guys, Thanks for all the help. I figured out what's wrong with the sequence 
file. 
I had accedently entered an "X' to one of the sub-chains.

Cheeres !
Gihan




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Re: [ccp4bb] CCP4BB vs COVID19

[Darren Hart]

Structure of 2019-nCov RNA polymerase:

https://www.biorxiv.org/content/10.1101/2020.03.16.993386v1.full.pdf+html

/Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in 
complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å...A 
comparative analysis to show how remdesivir binds to this polymerase is 
also provided. /


Darren



On 22/03/2020 19:18, Nikolay Dobrev wrote:

Dear all,
I assume most of you are aware of the EMBL-EBI datahub which was set 
up in January to provide essential virus research data to all 
scientists, but in case someone missed it I would like to share the link:

https://www.ebi.ac.uk/ena/pathogens/covid-19

You can find all relevant data, from COVID-19 genome sequencing data 
up to x-ray and cryo-EM structures of relevant proteins.


Stay healthy,
Nikolay

*Nikolay Dobrev *
Scientific Officer, Protein Expression and Purification Core Facility
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
T +49 6221 387 8633 | M +49 173 684 0532
twitter.com/EMBLorg <http://twitter.com/EMBLorg> | 
facebook.com/embl.org <http://facebook.com/embl.org> | 
youtube.com/user/emblmedia <http://youtube.com/user/emblmedia>
Visit www.embl.org/events <http://www.embl.org/events>for a complete 
list of all EMBL events.







On Sun, Mar 22, 2020 at 17:26, DUMAS Philippe (IGBMC) 
 wrote:


Relevant to the discussion:

* Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by
Cell Press
An RNA Thermosensor Controls Expression of Virulence Genes in
Listeria monocytogenes

* Bacterial RNA thermometers: molecular zippers and switches
Jens Kortmann and Franz Narberhaus
NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255

*An RNA Thermometer Activity of the West Nile Virus Genomic
30-Terminal Stem-Loop Element Modulates Viral Replication Eciency
during Host Switching
Viruses 2020, 12, 104; doi:10.3390/v12010104

* Temperature triggers immune evasion by Neisseria meningitidis
Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian
Zhang2, Bridget Gollan2, Helen Ewles2, Ronald Chalmers3,
Vladimir Pelicic2 & Christoph M. Tang1,2
Nature (2013)

Philippe Dumas

*De: *"James Holton" mailto:jmhol...@lbl.gov>>
*À: *"CCP4BB" mailto:CCP4BB@JISCMAIL.AC.UK>>
    *Envoyé: *Dimanche 22 Mars 2020 16:38:28
*Objet: *Re: [ccp4bb] CCP4BB vs COVID19

Thank you Patrick,

RNA structure is still structural biology, so I think relevant
here.  It seems to me that RNA as a thermometer would be an easy
hypothesis to test? Has anyone measured virulence vs temperature
in cell culture?

The 3D structure of the genome is no doublt important.  I wouldn't
want to try crystallizing the whole thing, but I wonder if this
might be an excellent target for cryoEM?  A challenge for that "we
can classify our way out of anything" philosophy?  And the result
would most certainly be interesting.

-James Holton
MAD Scientist

On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote:


James, this isn't conventional structural biology, but may be
of interest, and I haven't been able get any mainstream
virologists to think about it.

The protein sequences are obviously of interest, but so are
the RNA sequences at both ends of the Covid genome, which have
conserved secondary structure.  A few years ago a paper came
out suggesting that wild-type influenza has multiple "RNA
thermometers", which may play an important role in the tropism
of influenza.  Similar mechanisms may exist in other
respiratory viruses, including Covid.

My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick



https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


My paper in /Medical Hypotheses
/http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli
Chowdhury. "RNA thermometers." /FEMS microbiology
reviews/ 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced
perturbations of secondary mRNA structures are associated
with the cold-adapted temperature-sensitive phenotype of
influenza A virus." /RNA biology/ 9.10 (2012): 1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and
functions of coronavirus genomic 3′ and 5′ ends." /Virus
research/ 206 (2015): 120-133.



On Fri, Mar 20, 2020 at 10:59 PM James Holton
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structu

Re: [ccp4bb] CCP4BB vs COVID19

[Tristan Croll]

For what it’s worth, I’ve spent the last few days going over most of the 
existing COVID-19 related structures and rebuilding/re-refining wherever I 
considered necessary. The resulting models along with some basic explanatory 
notes are at 
https://drive.google.com/drive/folders/1S5qJtCnK00NrcbwwBNgImUMewhiBkyPa?usp=sharing.
 Some commentary on things I found can also be found in my Twitter thread at 
https://twitter.com/crolltristan/status/1241317484235554823?s=21. Normally I 
shy away from meddling with other people’s new models without invitation - but 
if ever there was a time to make an exception, this is it. Please feel free to 
use these for whatever purpose you like, and to improve on them further if you 
can. Tomorrow I’ll start personally contacting the individual authors to see if 
they’re willing to update their PDB entries.

Wishing the best of good health to all!

Tristan
 

 

> On 20 Mar 2020, at 22:59, James Holton  wrote:
> 
> You might think that as a structural biologist you won't be able to do much 
> about COVID-19 anytime soon, but that is not true.  Yes, real-world 
> therapeutics and vaccines take time, but we have already seen just how fast 
> we can get started.  There are 21 PDBs already and some even have bound 
> ligands.  Good job Frank et al. BTW!  And my personal thanks to all of you 
> out there who are already hard at work on this.
> 
> I believe this forum is an ideal place to share information and ideas on the 
> structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
> there are not that many proteins in it.  If all of us independently do the 
> same bioinformatics and literature searches and end up trying exactly the 
> same thing in every lab all over the world, then that would be more than 
> unfortunate.  To that end, I am personally interested on ORF8 for reasons I 
> will go into below.  Has anyone tried to solve it yet?  What happened?  
> Didn't express? Bad diffraction?  What?  Do tell.
> 
> Some of us, as you may have heard, are stuck at home, our beamlines and labs 
> dark while we shelter-in-place.  That doesn't mean our hands are tied.  We 
> are still allowed to think. The fraction of the human race that has a 
> snowball's chance in Hades of figuring out this bug is very very small.  
> Structure may be your main skill set, but you are still a biologist.  Do you 
> know how to run a PCR machine?  Do you know how to pipette?  You might think 
> that anybody can do it, but that is really not the case. Ever trained a new 
> student on sterile technique?  How many days did that take?  Now remember 
> that your student was no dummy and already studying biology.  Everyone 
> reading this will make an excellent volenteer at the very least.  I'm not 
> saying this to belittle the average human, only to say that we scientists, 
> moving in the circles we do, often forget that we have uncommon capabilities.
> 
> For example, I also believe we can be useful in assay development. The void 
> left by the dearth and delay of test results has been filled with fear, and 
> that is a big problem.  The tests, as defined, are straightforward, but also 
> extremely regimented like any good laboratory protocol should be.  The US 
> CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace 
> supplies, in high-throughput mode and still valid?  Not just for clinical but 
> for academic use?  I think more than a few people on this list could be 
> regarded as experts in making a complex biochemical task faster, more 
> efficient, high-throughput and nonetheless valid.  Yes, there are other 
> people who do virus testing for a living, but right now they are all rather 
> busy.  Maybe if we put our minds to it we can help?
> 
> As for why ORF8.  I am basing my interest on the bioinformatics done in this 
> article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
> will find what I'm talking about.  The authors found two "types" of 
> SARS-CoV-2.  They call them "S" and "L" because the only conserved amino acid 
> change involved is S84L in ORF8.  The "S" type is believed to be the ancestor 
> of "L".  What is interesting is how tightly linked this mutation is to a 
> silent mutation on the other end of the genome: the "L" type has a faster 
> codon for Ser in ORF1.  Such tight coupling (r^2=0.945) means there must be 
> significant selective pressure preventing both of these mutations occurring 
> in the same virus at the same time.  That, I believe, is interesting.  
> Espeically since they are so far apart I expect this selective pressure might 
> work in trans: as in a super-infection. That is, the S and L genome types may 
> interfere with each other.
> 
> The authors fall short of claiming evidence of interference upon 
> super-infection, and indeed they have already been criticised for calling "L" 
> the 

Re: [ccp4bb] CCP4BB vs COVID19

[Patrick Shaw Stewart]

James, there are lots of quite simple experiments that would be could be
done, but I can't get anyone to think seriously about the problem - let
alone do the experiments.

The attitude seems to be, "it can't be as simple as you suggest - someone
would have noticed it".

* Has anyone measured virulence vs temperature in cell culture?*


This isn't what you've got in mind, but yes, it was noticed that the
viruses that establish persistent infections of cell cultures (and they
have to be less aggressive to do that) often *spontaneously* become
temperature sensitive.  And, conversely, temperature-sensitive viruses that
are grown at low temp but in conditions where they can multiply fast, often
spontaneously lose their initial temperature-sensitivity.  Refs in my
paper.  Thse are all experiments that were done "by accident".

In influenza a temperature-driven switch has been seen, switching between
translation (high temp) and replication (low temp).  See the link below for
figures - described in words in my paper, below.

Best wishes

Patrick


Figures showing the "switch":
https://www.douglas.co.uk/f_ftp1/Seminar_by_Patrick_Shaw_Stewart_-_a_few_slides_for_Bill.pdf
Paper: http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf
Easy read part 1, about seasonality: https://oldwivesandvirologists.blog/
Easy read part 2 about Covid:
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


_


>From my paper:


*The temperature sensitivity of viral transcription*

Most laboratory respiratory viruses are propagated at 37 C, which may
result in the rapid
loss of ts characters, especially since viruses mutate very rapidly when
they are introduced
to new hosts. If, however, temperature sensitivity is a common feature of
wild respiratory
viruses, we might expect to see remnants of temperature sensitivity in the
biochemistry
of laboratory strains. It turns out that such remnants are quite common.
For several
decades virologists have found that maximum RNA transcription in influenza
viruses occurs
below normal body temperature. In 1977, Plotch and Krug [61] reported that
the greatest
activity of the RNA polymerase of WSN virus was at 30–32 C. This is similar
to the optimum
temperature of the polymerase of influenza C, which is 33 C [62,63].
Ulmanen et al. [64]
found that the rate of transcription by detergent-treated WSN viruses
(influenza A) was about
10 times greater at 33 C than at 39.5 C, and also that the binding of a
cleaved primer cap
(the ‘‘A13 fragment”) to the viral cores was ‘‘unexpectedly” much weaker at
39.5 C than at
33 C. Scholtissek and Rott [65] showed that the optimum for the polymerase
of the
Rostock strain of fowl plague virus was 36 C, five degrees below chickens’
normal body
temperature (41 C). At least two reports show that temperature affects the
balance between
transcription and viral replication. Kashiwagi et al. looked at the effect
of temperature on
RNA production for five varied influenza A strains [66]. For all strains,
vRNA unexpectedly
decreased when the temperature was increased from 37 C to 42 C. The PA
subunit of the
viral polymerase caused this thermal sensitivity. In another interesting
study, Dalton et al.
showed that the production of mRNA by the PR8 influenza strain is favored
at a higher
temperature (41 C), with very little vRNA being produced at that
temperature [67]. A plasmid-
based recombinant system showed that as the incubation temperature
increased from 31 C
to 39 C the amount of replicative RNA products (c- and vRNA) decreased and
a greater
accumulation of mRNA was observed. The cRNA that is used as a template to
make the
vRNA formed a complex with the polymerase that was particularly
heat-labile, showing rapid
dissociation even at 37 C. The authors suggested that the ‘‘switch” that
regulates the
transition from transcription to replication is dependent on temperature,
but made no
comments about how shifts in the host’s body or respiratory tract
temperature may influence
this transition.





On Sun, Mar 22, 2020 at 3:38 PM James Holton  wrote:

> Thank you Patrick,
>
> RNA structure is still structural biology, so I think relevant here.  It
> seems to me that RNA as a thermometer would be an easy hypothesis to test?
> Has anyone measured virulence vs temperature in cell culture?
>
> The 3D structure of the genome is no doublt important.  I wouldn't want to
> try crystallizing the whole thing, but I wonder if this might be an
> excellent target for cryoEM?  A challenge for that "we can classify our way
> out of anything" philosophy?  And the result would most certainly be
> interesting.
>
> -James Holton
> MAD Scientist
>
> On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote:
>
>
> James, this isn't conventional structural biology, but may be of interest,
> and I haven't been able get any mainstream virologists to think about it.
>
> The protein sequences are obviously of interest, but so are the RNA
> sequences at 

Re: [ccp4bb] CCP4BB vs COVID19

[Nikolay Dobrev]

Dear all,
I assume most of you are aware of the EMBL-EBI datahub which was set up in 
January to provide essential virus research data to all scientists, but in case 
someone missed it I would like to share the link:
https://www.ebi.ac.uk/ena/pathogens/covid-19 
(https://www.ebi.ac.uk/ena/pathogens/covid-19)
You can find all relevant data, from COVID-19 genome sequencing data up to 
x-ray and cryo-EM structures of relevant proteins.
Stay healthy,
Nikolay
Nikolay Dobrev 
Scientific Officer, Protein Expression and Purification Core Facility
EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
T +49 6221 387 8633 | M +49 173 684 0532
twitter.com/EMBLorg (http://twitter.com/EMBLorg) | facebook.com/embl.org 
(http://facebook.com/embl.org) | youtube.com/user/emblmedia 
(http://youtube.com/user/emblmedia)
Visit www.embl.org/events (http://www.embl.org/events) for a complete list of 
all EMBL events.
On Sun, Mar 22, 2020 at 17:26, DUMAS Philippe (IGBMC)  wrote: 
Relevant to the discussion:
* Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press
An RNA Thermosensor Controls Expression of Virulence Genes in Listeria 
monocytogenes
* Bacterial RNA thermometers: molecular zippers and switches
Jens Kortmann and Franz Narberhaus
NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255
*An RNA Thermometer Activity of the West Nile Virus Genomic 30-Terminal 
Stem-Loop Element Modulates Viral Replication Eciency during Host Switching
Viruses 2020, 12, 104; doi:10.3390/v12010104
* Temperature triggers immune evasion by Neisseria meningitidis

Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget 
Gollan2, Helen Ewles2, Ronald Chalmers3,
Vladimir Pelicic2 & Christoph M. Tang1,2
Nature (2013)
Philippe Dumas

De: "James Holton" 
À: "CCP4BB" 
Envoyé: Dimanche 22 Mars 2020 16:38:28
Objet: Re: [ccp4bb] CCP4BB vs COVID19
Thank you Patrick,

 RNA structure is still structural biology, so I think relevant here.  It seems 
to me that RNA as a thermometer would be an easy hypothesis to test?  Has 
anyone measured virulence vs temperature in cell culture?  

 The 3D structure of the genome is no doublt important.  I wouldn't want to try 
crystallizing the whole thing, but I wonder if this might be an excellent 
target for cryoEM?  A challenge for that "we can classify our way out of 
anything" philosophy?  And the result would most certainly be interesting.

 -James Holton
 MAD Scientist
On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote:
 James, this isn't conventional structural biology, but may be of interest, and 
I haven't been able get any mainstream virologists to think about it. 
The protein sequences are obviously of interest, but so are the RNA sequences 
at both ends of the Covid genome, which have conserved secondary structure.  A 
few years ago a paper came out suggesting that wild-type influenza has multiple 
"RNA thermometers", which may play an important role in the tropism of 
influenza.  Similar mechanisms may exist in other respiratory viruses, 
including Covid. 
My take on this, and the relevant papers, are below. 
Good luck to everyone and stay well,  
Patrick 
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
 
(https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/)

My paper in Medical Hypotheses 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf 
(http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf)
Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA 
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.
Chursov, Andrey, et al. "Specific temperature-induced perturbations of 
secondary mRNA structures are associated with the cold-adapted 
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 
1266-1274.
Yang, Dong, and Julian L. Leibowitz. "The structure and functions of 
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.   
 On Fri, Mar 20, 2020 at 10:59 PM James Holton  wrote:
 You might think that as a structural biologist you won't be able to do 
 much about COVID-19 anytime soon, but that is not true.  Yes, real-world 
 therapeutics and vaccines take time, but we have already seen just how 
 fast we can get started.  There are 21 PDBs already and some even have 
 bound ligands.  Good job Frank et al. BTW!  And my personal thanks to 
 all of you out there who are already hard at work on this.

 I believe this forum is an ideal place to share information and ideas on 
 the structural biology of SARS-CoV-2 as we move forward. It's a big 
 virus, but there are not that many proteins in it.  If all of us 
 independently do the same bioinformatics and literature searches and end 
 up trying exactly the same thing in every lab all over the world, then 
 that would be more than unfortunate.  To that 

Re: [ccp4bb] CCP4BB vs COVID19

[DUMAS Philippe (IGBMC)]

Relevant to the discussion: 

* Cell, Vol. 110, 551–561, September 6, 2002, Copyright 2002 by Cell Press 
An RNA Thermosensor Controls Expression of Virulence Genes in Listeria 
monocytogenes 

* Bacterial RNA thermometers: molecular zippers and switches 
Jens Kortmann and Franz Narberhaus 
NATURE REVIEWS | MICROBIOLOGY VOLUME 10 | APRIL 2012 | 255 

*An RNA Thermometer Activity of the West Nile Virus Genomic 30-Terminal 
Stem-Loop Element Modulates Viral Replication Eciency during Host Switching 
Viruses 2020, 12, 104; doi:10.3390/v12010104 

* Temperature triggers immune evasion by Neisseria meningitidis 
Edmund Loh1*, Elisabeth Kugelberg2*, Alexander Tracy1, Qian Zhang2, Bridget 
Gollan2, Helen Ewles2, Ronald Chalmers3, 
Vladimir Pelicic2 & Christoph M. Tang1,2 
Nature (2013) 

Philippe Dumas 

De: "James Holton"  
À: "CCP4BB"  
Envoyé: Dimanche 22 Mars 2020 16:38:28 
Objet: Re: [ccp4bb] CCP4BB vs COVID19 

Thank you Patrick, 

RNA structure is still structural biology, so I think relevant here. It seems 
to me that RNA as a thermometer would be an easy hypothesis to test? Has anyone 
measured virulence vs temperature in cell culture? 

The 3D structure of the genome is no doublt important. I wouldn't want to try 
crystallizing the whole thing, but I wonder if this might be an excellent 
target for cryoEM? A challenge for that "we can classify our way out of 
anything" philosophy? And the result would most certainly be interesting. 

-James Holton 
MAD Scientist 

On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote: 




James, this isn't conventional structural biology, but may be of interest, and 
I haven't been able get any mainstream virologists to think about it. 

The protein sequences are obviously of interest, but so are the RNA sequences 
at both ends of the Covid genome, which have conserved secondary structure. A 
few years ago a paper came out suggesting that wild-type influenza has multiple 
"RNA thermometers", which may play an important role in the tropism of 
influenza. Similar mechanisms may exist in other respiratory viruses, including 
Covid. 

My take on this, and the relevant papers, are below. 

Good luck to everyone and stay well, 

Patrick 



BQ_BEGIN

[ 
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
 | 
https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
 ] 

My paper in Medical Hypotheses [ 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf | 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf ] 

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA 
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16. 

Chursov, Andrey, et al. "Specific temperature-induced perturbations of 
secondary mRNA structures are associated with the cold-adapted 
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 
1266-1274. 

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of 
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133. 





On Fri, Mar 20, 2020 at 10:59 PM James Holton < [ mailto:jmhol...@lbl.gov | 
jmhol...@lbl.gov ] > wrote: 

BQ_BEGIN
You might think that as a structural biologist you won't be able to do 
much about COVID-19 anytime soon, but that is not true. Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how 
fast we can get started. There are 21 PDBs already and some even have 
bound ligands. Good job Frank et al. BTW! And my personal thanks to 
all of you out there who are already hard at work on this. 

I believe this forum is an ideal place to share information and ideas on 
the structural biology of SARS-CoV-2 as we move forward. It's a big 
virus, but there are not that many proteins in it. If all of us 
independently do the same bioinformatics and literature searches and end 
up trying exactly the same thing in every lab all over the world, then 
that would be more than unfortunate. To that end, I am personally 
interested on ORF8 for reasons I will go into below. Has anyone tried 
to solve it yet? What happened? Didn't express? Bad diffraction? 
What? Do tell. 

Some of us, as you may have heard, are stuck at home, our beamlines and 
labs dark while we shelter-in-place. That doesn't mean our hands are 
tied. We are still allowed to think. The fraction of the human race 
that has a snowball's chance in Hades of figuring out this bug is very 
very small. Structure may be your main skill set, but you are still a 
biologist. Do you know how to run a PCR machine? Do you know how to 
pipette? You might think that anybody can do it, but that is really not 
the case. Ever trained a new student on sterile technique? How many 
days did that take? Now remember that your student was no dummy and 
already studying biology. Everyone reading this will make an excellent 
volenteer at the very least. I'm not sa

Re: [ccp4bb] CCP4BB vs COVID19

[James Holton]

Thank you Patrick,

RNA structure is still structural biology, so I think relevant here.  It 
seems to me that RNA as a thermometer would be an easy hypothesis to 
test?  Has anyone measured virulence vs temperature in cell culture?


The 3D structure of the genome is no doublt important.  I wouldn't want 
to try crystallizing the whole thing, but I wonder if this might be an 
excellent target for cryoEM?  A challenge for that "we can classify our 
way out of anything" philosophy?  And the result would most certainly be 
interesting.


-James Holton
MAD Scientist

On 3/21/2020 8:41 AM, Patrick Shaw Stewart wrote:


James, this isn't conventional structural biology, but may be of 
interest, and I haven't been able get any mainstream virologists to 
think about it.


The protein sequences are obviously of interest, but so are the RNA 
sequences at both ends of the Covid genome, which have conserved 
secondary structure.  A few years ago a paper came out suggesting that 
wild-type influenza has multiple "RNA thermometers", which may play an 
important role in the tropism of influenza.  Similar mechanisms may 
exist in other respiratory viruses, including Covid.


My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick



https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


My paper in /Medical Hypotheses
/http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury.
"RNA thermometers." /FEMS microbiology reviews/ 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced
perturbations of secondary mRNA structures are associated with the
cold-adapted temperature-sensitive phenotype of influenza A
virus." /RNA biology/ 9.10 (2012): 1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions
of coronavirus genomic 3′ and 5′ ends." /Virus research/ 206
(2015): 120-133.



On Fri, Mar 20, 2020 at 10:59 PM James Holton > wrote:


You might think that as a structural biologist you won't be able
to do
much about COVID-19 anytime soon, but that is not true. Yes,
real-world
therapeutics and vaccines take time, but we have already seen just
how
fast we can get started.  There are 21 PDBs already and some even
have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and
ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches
and end
up trying exactly the same thing in every lab all over the world,
then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone
tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our
beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is
very
very small.  Structure may be your main skill set, but you are
still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is
really not
the case. Ever trained a new student on sterile technique? How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an
excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the
circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development.
The
void left by the dearth and delay of test results has been filled
with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good
laboratory
protocol should be.  The US CDC's instructions for academic labs
are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more
commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on
this
list could be regarded as experts in making a complex biochemical
task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other 

Re: [ccp4bb] CCP4BB vs COVID19

[James Holton]

Well, look at that!  I had missed that one.  Thank you Dan.

Ahh, those Ig folds.  They are like dougnuts.  Is there anything they 
can't do?


Interesting that Tan et al. arrived at their conclusions from a very 
different line of evidence.  They seem to have missed the covariance 
with the silent site pointed out by Tang et al.?


1xak is from original SARS, and I must say not great statistics despite 
being at 1.8A.  Still, it is a start.


From the literature cited by Tan et al. it appears ORF8 has been 
suspected as pathogenic for some time, but for widely different 
reasons.  One paper says it is a transcription factor that up-regulates 
chaperones, another says it is a secreted imunosuppressor.


So, my question remains: why haven't we solved it yet?

-James Holton
MAD Scientist

On 3/21/2020 9:12 AM, Rigden, Dan wrote:


Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. 
In fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like 
fold similar to ORF7 (for which there is a structure; 1xak).



https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this 
pre-print which tells the whole story very nicely, including that key 
position 84



https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1

Best wishes

Dan


*From:* CCP4 bulletin board  on behalf of 
Patrick Shaw Stewart 

*Sent:* 21 March 2020 15:41:17
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] CCP4BB vs COVID19

James, this isn't conventional structural biology, but may be of 
interest, and I haven't been able get any mainstream virologists to 
think about it.


The protein sequences are obviously of interest, but so are the RNA 
sequences at both ends of the Covid genome, which have conserved 
secondary structure.  A few years ago a paper came out suggesting that 
wild-type influenza has multiple "RNA thermometers", which may play an 
important role in the tropism of influenza.  Similar mechanisms may 
exist in other respiratory viruses, including Covid.


My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick



https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


My paper in /Medical Hypotheses
/http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury.
"RNA thermometers." /FEMS microbiology reviews/ 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced
perturbations of secondary mRNA structures are associated with the
cold-adapted temperature-sensitive phenotype of influenza A
virus." /RNA biology/ 9.10 (2012): 1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions
of coronavirus genomic 3′ and 5′ ends." /Virus research/ 206
(2015): 120-133.



On Fri, Mar 20, 2020 at 10:59 PM James Holton <mailto:jmhol...@lbl.gov>> wrote:


You might think that as a structural biologist you won't be able
to do
much about COVID-19 anytime soon, but that is not true. Yes,
real-world
therapeutics and vaccines take time, but we have already seen just
how
fast we can get started.  There are 21 PDBs already and some even
have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and
ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches
and end
up trying exactly the same thing in every lab all over the world,
then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone
tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our
beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is
very
very small.  Structure may be your main skill set, but you are
still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is
really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an
excellent
volenteer at the very least.  I'm not saying th

Re: [ccp4bb] CCP4BB vs COVID19

[Chandra]

hi

There are developments in cyclic and constrained peptides

see for example J Am Chem Soc. 
<https://www.ncbi.nlm.nih.gov/pubmed/30768253#>2019 Mar 
13;141(10):4167-4181.


hope it helps


On 22/3/2020 8:01 pm, Abhishek Anan wrote:

Dear all,

Not directly related to the discussion but does anyone know of a
antiretroviral protease inhibitor that is a peptide? I am new to the
topic and read that peptides suffer from bioavailability issues. Are
there any workarounds?

best,
Abhishek


On 3/21/20, Rigden, Dan  wrote:

Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In
fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold
similar to ORF7 (for which there is a structure; 1xak).


https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this pre-print
which tells the whole story very nicely, including that key position 84


https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1


Best wishes

Dan


From: CCP4 bulletin board  on behalf of Patrick Shaw
Stewart 
Sent: 21 March 2020 15:41:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB vs COVID19


James, this isn't conventional structural biology, but may be of interest,
and I haven't been able get any mainstream virologists to think about it.

The protein sequences are obviously of interest, but so are the RNA
sequences at both ends of the Covid genome, which have conserved secondary
structure.  A few years ago a paper came out suggesting that wild-type
influenza has multiple "RNA thermometers", which may play an important role
in the tropism of influenza.  Similar mechanisms may exist in other
respiratory viruses, including Covid.

My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick


https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/

My paper in Medical Hypotheses
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced perturbations of
secondary mRNA structures are associated with the cold-adapted
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10
(2012): 1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.



On Fri, Mar 20, 2020 at 10:59 PM James Holton
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be m

Re: [ccp4bb] CCP4BB vs COVID19

[Abhishek Anan]

Dear all,

Not directly related to the discussion but does anyone know of a
antiretroviral protease inhibitor that is a peptide? I am new to the
topic and read that peptides suffer from bioavailability issues. Are
there any workarounds?

best,
Abhishek


On 3/21/20, Rigden, Dan  wrote:
> Hi James
>
>
> 5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In
> fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold
> similar to ORF7 (for which there is a structure; 1xak).
>
>
> https://toolkit.tuebingen.mpg.de/jobs/2717885_1
>
>
> I must say I got quite excited seeing that until I noticed this pre-print
> which tells the whole story very nicely, including that key position 84
>
>
> https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1
>
>
> Best wishes
>
> Dan
>
> 
> From: CCP4 bulletin board  on behalf of Patrick Shaw
> Stewart 
> Sent: 21 March 2020 15:41:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] CCP4BB vs COVID19
>
>
> James, this isn't conventional structural biology, but may be of interest,
> and I haven't been able get any mainstream virologists to think about it.
>
> The protein sequences are obviously of interest, but so are the RNA
> sequences at both ends of the Covid genome, which have conserved secondary
> structure.  A few years ago a paper came out suggesting that wild-type
> influenza has multiple "RNA thermometers", which may play an important role
> in the tropism of influenza.  Similar mechanisms may exist in other
> respiratory viruses, including Covid.
>
> My take on this, and the relevant papers, are below.
>
> Good luck to everyone and stay well,
>
> Patrick
>
>
> https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
>
> My paper in Medical Hypotheses
> http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf
>
> Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA
> thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.
>
> Chursov, Andrey, et al. "Specific temperature-induced perturbations of
> secondary mRNA structures are associated with the cold-adapted
> temperature-sensitive phenotype of influenza A virus." RNA biology 9.10
> (2012): 1266-1274.
>
> Yang, Dong, and Julian L. Leibowitz. "The structure and functions of
> coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.
>
>
>
> On Fri, Mar 20, 2020 at 10:59 PM James Holton
> mailto:jmhol...@lbl.gov>> wrote:
> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straight

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Michel Fodje]

In Ascoidea asiatica where CUG is translated as both Leu and Ser.
Mühlhausen S., Schmitt H.D., Pan K.T., Plessmann U., Urlaub H., Hurst L.D., 
Kollmar M. Endogenous stochastic decoding of the CUG codon by competing Ser- 
and Leu-tRNAs in Ascoidea asiatica. Curr. Biol. 2018; 28:2046-2057.

Perhaps, this is not a mutation at all but points to the origin of this virus.

/Michel.

From: CCP4 bulletin board  On Behalf Of Carter, Charlie
Sent: March 21, 2020 7:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19




Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is

Re: [ccp4bb] CCP4BB vs COVID19

[Rigden, Dan]

Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In fact, 
rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold similar to 
ORF7 (for which there is a structure; 1xak).


https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this pre-print which 
tells the whole story very nicely, including that key position 84


https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1


Best wishes

Dan


From: CCP4 bulletin board  on behalf of Patrick Shaw 
Stewart 
Sent: 21 March 2020 15:41:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB vs COVID19


James, this isn't conventional structural biology, but may be of interest, and 
I haven't been able get any mainstream virologists to think about it.

The protein sequences are obviously of interest, but so are the RNA sequences 
at both ends of the Covid genome, which have conserved secondary structure.  A 
few years ago a paper came out suggesting that wild-type influenza has multiple 
"RNA thermometers", which may play an important role in the tropism of 
influenza.  Similar mechanisms may exist in other respiratory viruses, 
including Covid.

My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick


https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/

My paper in Medical Hypotheses 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA 
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced perturbations of 
secondary mRNA structures are associated with the cold-adapted 
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 
1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of 
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.



On Fri, Mar 20, 2020 at 10:59 PM James Holton 
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on this
list could be regarded as experts in making a complex biochemical task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other people who do virus testing for a living, but right now
they are all rather busy.  Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinform

Re: [ccp4bb] CCP4BB vs COVID19

[Patrick Shaw Stewart]

James, this isn't conventional structural biology, but may be of interest,
and I haven't been able get any mainstream virologists to think about it.

The protein sequences are obviously of interest, but so are the RNA
sequences at both ends of the Covid genome, which have conserved secondary
structure.  A few years ago a paper came out suggesting that wild-type
influenza has multiple "RNA thermometers", which may play an important role
in the tropism of influenza.  Similar mechanisms may exist in other
respiratory viruses, including Covid.

My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick


https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


My paper in *Medical Hypotheses *
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA
thermometers." *FEMS microbiology reviews* 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced perturbations of
secondary mRNA structures are associated with the cold-adapted
temperature-sensitive phenotype of influenza A virus." *RNA biology* 9.10
(2012): 1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of
coronavirus genomic 3′ and 5′ ends." *Virus research* 206 (2015): 120-133.




On Fri, Mar 20, 2020 at 10:59 PM James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is interesting.  Espeically since 
they are so far apart I expect this selective pressure might work in trans: as 
in a super-infection. That is, the S and L genome types may interfere with each 
other.

The authors fall short of claiming evidence of interference upon 
super-infection, and indeed they have already been criticised for calling "L" 
the "aggressive" type.  But it is still interesting and points a finger at ORF8.

ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch of 
60 residues.  This homolog

Re: [ccp4bb] CCP4BB vs COVID19

[Boy]

The best way against COVID19 is staying at home, staying at home, and
staying at home.

Nothing else.

On Fri, Mar 20, 2020, 5:59 PM James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  That, I believe, is interesting.  Espeically since they are
> so far apart I expect this selective pressure might work in trans: as in
> a super-infection. That is, the S and L genome types may interfere with
> each other.
>
> The authors fall short of claiming evidence of interference upon
> super-infection, and indeed they have already been criticised for
> calling "L" the "aggressive" type.  But it is still interesting and
> points a finger at ORF8.
>
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a
> stretch of 60 residues.  This homologous region contains the S84L site
> (Val I544 in 5o32).  I had a quick look and appears to be a
> cavity-filling mutation to me.  Not very big, but maybe something could
> fit in there.  To be sure we'd need a structure of ORF8.
>
> Good luck to you all, and stay healthy.
>
> -James Holton
> MAD Scientist
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] CCP4BB vs COVID19

[Clemens Vonrhein]

Dear James,

On Fri, Mar 20, 2020 at 03:59:01PM -0700, James Holton wrote:
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch
> of 60 residues.  This homologous region contains the S84L site (Val I544 in
> 5o32).  I had a quick look and appears to be a cavity-filling mutation to
> me.  Not very big, but maybe something could fit in there.  To be sure we'd
> need a structure of ORF8.

This is a very good example of why we all are trying to get raw
diffraction data deposited as soon as possible to the publication and
deposition of a structure. It highlights the potential benefit of
revisting some important structures right at the level of the raw
data. The paper says

  Diffraction data were collected at European Synchrotron Radiation
  Facility (ESRF) and Swiss Light Source at Paul Scherrer Institute
  (SLS-PSI). Diffraction data were processed by XDS and
  AIMLESS. Crystals of C3b–miniFH–FI exhibited space group P1 and
  diffracted to a resolution of 3.8 Å. However, the diffraction data
  was highly anisotropic. The data were therefore truncated to 4.2-Å
  resolution and rescaled using the Diffraction Anisotropy Server.

Obviously, that was state-of-the-art in 2015 (data collection) and
2017 (publication) - but maybe new methods could indeed do better on
this already existing structure if the raw data became
available. Maybe nothing will change in terms of structure quality and
(most importantly) structure interpretation ... who knows.

We've contacted the authors - who were very quick and extremely
helpful in providing us with raw images for some other deposited
project from their lab a few weeks ago, so expect and hope for a
similar response when/if the data can be located.

> Good luck to you all, and stay healthy.

Ditto!

Cheers

Clemens

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] CCP4BB vs COVID19

[Paula Salgado]

Same for Newcastle University, particularly our Faculty of Medical Sciences but 
colleagues and labs from across the University.

There are also several efforts to get scientists to help:

http://crowdfightcovid19.org/volunteers

Thanks to all those trying to help!

Paula



On 21 Mar 2020, at 11:53, David Briggs  wrote:


For general interest,

The Francis Crick institute in London is offering facilities to public health 
England, and over 300 Crick scientists have volunteered to help with testing.

https://www.crick.ac.uk/news/2020-03-19_francis-crick-institute-offers-assistance-in-emergency-coronavirus-testing

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of David Waterman 

Sent: Saturday, March 21, 2020 11:12:36 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help 
fill the testing shortfall in the UK (see 
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wired.co.uk%2Farticle%2Fcoronavirus-uk-testing-key-workers=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=M4TnA9YFRaRkCO%2B7MtI1prS615g8Ff0VWWnrMWArv8s%3D=0>).
 This is a worthy initiative, if it is accepted (logistics are the main 
problem). The structural biology community is pretty good with this too. 
Perhaps there are some opportunities to help out here, for those who can still 
get to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton 
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-nCoV%2Flab%2Findex.html=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=nLlQqA10Uh5JWPRACl5ofZotvzRhTR0XimeWiNCZ4GI%3D=0>
My question is: how can this test be made faster, using more commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on this
list could be regarded as experts in making a complex biochemical task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other people who do virus testing for a living, but right now
they are all rather busy.  Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in
this article: 
https://dx.d

Re: [ccp4bb] CCP4BB vs COVID19

[David Briggs]

For general interest,

The Francis Crick institute in London is offering facilities to public health 
England, and over 300 Crick scientists have volunteered to help with testing.

https://www.crick.ac.uk/news/2020-03-19_francis-crick-institute-offers-assistance-in-emergency-coronavirus-testing

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of David Waterman 

Sent: Saturday, March 21, 2020 11:12:36 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help 
fill the testing shortfall in the UK (see 
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wired.co.uk%2Farticle%2Fcoronavirus-uk-testing-key-workers=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=M4TnA9YFRaRkCO%2B7MtI1prS615g8Ff0VWWnrMWArv8s%3D=0>).
 This is a worthy initiative, if it is accepted (logistics are the main 
problem). The structural biology community is pretty good with this too. 
Perhaps there are some opportunities to help out here, for those who can still 
get to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton 
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-nCoV%2Flab%2Findex.html=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739921917=nLlQqA10Uh5JWPRACl5ofZotvzRhTR0XimeWiNCZ4GI%3D=0>
My question is: how can this test be made faster, using more commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on this
list could be regarded as experts in making a complex biochemical task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other people who do virus testing for a living, but right now
they are all rather busy.  Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in
this article: 
https://dx.doi.org/10.1093/nsr/nwaa036<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdx.doi.org%2F10.1093%2Fnsr%2Fnwaa036=02%7C01%7C%7Cde0d51b4b5e54708671d08d7cd88cc25%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C0%7C637203859739931914=g%2Fv1diPmPWKEo%2Frw371ZRUgl%2BGEGJHxGj6kaSLxjAas%3D=0>.
  Search for
"T8517

Re: [ccp4bb] CCP4BB vs COVID19

[David Waterman]

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to
help fill the testing shortfall in the UK (see
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers). This
is a worthy initiative, if it is accepted (logistics are the main problem).
The structural biology community is pretty good with this too. Perhaps
there are some opportunities to help out here, for those who can still get
to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  That, I believe, is interesting.  Espeically since they are
> so far apart I expect this selective pressure might work in trans: as in
> a super-infection. That is, the S and L genome types may interfere with
> each other.
>
> The authors fall short of claiming evidence of interference upon
> super-infection, and indeed they have already been criticised for
> calling "L" the "aggressive" type.  But it is still interesting and
> points a finger at ORF8.
>
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a
> stretch of 60 residues.  This homologous region contains the S84L site
> (Val I544 in 5o32).  I had a quick look and appears to be a
> cavity-filling mutation to me.  Not very big, but maybe something could
> fit in there.  To be sure we'd need a structure of ORF8.
>
> Good luck to you all, and stay healthy.
>
> -James Holton
> MAD Scientist
>
> 

[ccp4bb] CCP4BB vs COVID19

[James Holton]

You might think that as a structural biologist you won't be able to do 
much about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how 
fast we can get started.  There are 21 PDBs already and some even have 
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to 
all of you out there who are already hard at work on this.


I believe this forum is an ideal place to share information and ideas on 
the structural biology of SARS-CoV-2 as we move forward. It's a big 
virus, but there are not that many proteins in it.  If all of us 
independently do the same bioinformatics and literature searches and end 
up trying exactly the same thing in every lab all over the world, then 
that would be more than unfortunate.  To that end, I am personally 
interested on ORF8 for reasons I will go into below.  Has anyone tried 
to solve it yet?  What happened?  Didn't express? Bad diffraction?  
What?  Do tell.


Some of us, as you may have heard, are stuck at home, our beamlines and 
labs dark while we shelter-in-place.  That doesn't mean our hands are 
tied.  We are still allowed to think. The fraction of the human race 
that has a snowball's chance in Hades of figuring out this bug is very 
very small.  Structure may be your main skill set, but you are still a 
biologist.  Do you know how to run a PCR machine?  Do you know how to 
pipette?  You might think that anybody can do it, but that is really not 
the case. Ever trained a new student on sterile technique?  How many 
days did that take?  Now remember that your student was no dummy and 
already studying biology.  Everyone reading this will make an excellent 
volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we 
do, often forget that we have uncommon capabilities.


For example, I also believe we can be useful in assay development. The 
void left by the dearth and delay of test results has been filled with 
fear, and that is a big problem.  The tests, as defined, are 
straightforward, but also extremely regimented like any good laboratory 
protocol should be.  The US CDC's instructions for academic labs are here:

https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for 
clinical but for academic use?  I think more than a few people on this 
list could be regarded as experts in making a complex biochemical task 
faster, more efficient, high-throughput and nonetheless valid.  Yes, 
there are other people who do virus testing for a living, but right now 
they are all rather busy.  Maybe if we put our minds to it we can help?


As for why ORF8.  I am basing my interest on the bioinformatics done in 
this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for 
"T8517C" and you will find what I'm talking about.  The authors found 
two "types" of SARS-CoV-2.  They call them "S" and "L" because the only 
conserved amino acid change involved is S84L in ORF8.  The "S" type is 
believed to be the ancestor of "L".  What is interesting is how tightly 
linked this mutation is to a silent mutation on the other end of the 
genome: the "L" type has a faster codon for Ser in ORF1.  Such tight 
coupling (r^2=0.945) means there must be significant selective pressure 
preventing both of these mutations occurring in the same virus at the 
same time.  That, I believe, is interesting.  Espeically since they are 
so far apart I expect this selective pressure might work in trans: as in 
a super-infection. That is, the S and L genome types may interfere with 
each other.


The authors fall short of claiming evidence of interference upon 
super-infection, and indeed they have already been criticised for 
calling "L" the "aggressive" type.  But it is still interesting and 
points a finger at ORF8.


ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a 
stretch of 60 residues.  This homologous region contains the S84L site 
(Val I544 in 5o32).  I had a quick look and appears to be a 
cavity-filling mutation to me.  Not very big, but maybe something could 
fit in there.  To be sure we'd need a structure of ORF8.


Good luck to you all, and stay healthy.

-James Holton
MAD Scientist



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] CCP4BB Digest - 27 Feb 2020 to 28 Feb 2020 (#2020-61)

[Phoebe A. Rice]

While we're at it, it would also be a great improvement if the PDB would list 
nominal resolution in all 3 directions for structures with significantly 
anisotropic data.  I'm never 100% sure what to do in those cases.
 Thanks, 
 Phoebe

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/
 

On 3/1/20, 5:19 PM, "CCP4 bulletin board on behalf of dusan turk" 
 wrote:

Hi again,

First, I wish to thank everyone for their responses. I hope that no one 
minds that I include them in my response letter to the Editor ?

The idea of citing the Karplus and Diedrichs paper in Science has been 
essentially consumed already in our first response letter, which accompanied 
the submission of the revised manuscript,  and did not work. (Instead of the 
Science citation from 2012 we used a quote from the paper suggested below by 
Karplus and Diederichs, Curr Opin Struct Biol. 2015 Oct; 34: 60–68. )

As Phoebe mentioned, it would be good to use the momentum. My intention of 
writing to the bulletin board was not only to get help with argumentation, but 
also to raise the issue of how to address resolution cutoffs in 
crystallographic data in publications  to avoid such situations in general. I 
also think that the issue is more complicated than the last shell criterion 
with I/Isig > xx, Rmerge < yy, or cc1/2 > zz, or ...

1. Number of reflections in a shell effects the numbers significantly. The 
larger numbers of the shells there are the larger the numbers will be.  The 
number of reflections in a shell depends also on the highest resolution and 
unit cell size. Hence we have a dependance of potential criteria on several 
parameters. 

2. Refinement and data processing programs use different numbers of shells 
and even different ways of calculating shells. REFMAC typically uses 20 equal 
volume sliced shells), PHENIX is more complicated, as far as I understand 
(shell number may depend on the number of TEST set reflections in individual 
shell, shells can be defined according to equal  slicing volume,  some kind of 
log dependency or even linearly according to real space resolution), in MAIN 
there are  20 shells by default, but one can choose any of the mentioned 
slicing rules.

I suggest that we use this discussion to shape up guidelines that can later 
proposed for consideration to the IUCr committee for macromolecules.  I prefer 
soft as opposed to strict borders.  In the end, the structures do not speak for 
themselves, but are a mean to support one or more biologically relevant 
conclusions.

???

best wishes,
dusan turk


> On 29 Feb 2020, at 01:00, CCP4BB automatic digest system 
 wrote:
> 
> 
> Date:Fri, 28 Feb 2020 16:03:22 +
> From:"Phoebe A. Rice" 
> Subject: Re: What resolution - X-ray diffraction round this time
> 
> Can we get some momentum for the "standard table 1" including TWO numbers 
- outer limit used in refinement, and nominal resolution based on some standard 
such as I/sigI =2 (or 3, or whatever the community can agree on)? That would 
hopefully cut down on all the reviewer complaints of overstated resolution.
> 
> ~~~
> Phoebe A. Rice
> Dept. of Biochem & Mol. Biol. and
>  Committee on Microbiology
> https://voices.uchicago.edu/phoebericelab/
> 
> 
> On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" 
 wrote:
> 
>Dear colleagues,
> 
>I agree with all the previous responses, it is a pity to throw away
>useful high-resolution data. The problem of high-resolution cutoff
>estimation is also nicely summarized in another paper by Andrew Karplus
>and Kay Diederichs "Assessing and maximizing data quality in
>macromolecular crystallography"
>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ . It is suggested
>using CC1/2 for the selection of the cutoff for data processing (not
>I/sigI or R_whatever). Later on, the decision should be validated
>performing the paired refinement protocol.
> 
>Good luck with the argumentation.
>Martin
> 
> 
>On 2/28/20 11:08 AM, LMB wrote:
>> Ask the referee - (apart from the other suggestions here)
>> 
>> ‘How would removing data Improve my model?”
>> 
>> Sent from my iPad
>> 
>>> On 28 Feb 2020, at 08:22, dusan turk  wrote:
>>> 
>>> Hi,
>>> 
>>> Browsing through the recent discussion on EM data resolution cutoff
>>> it occurred to me that the X-ray diffraction community isn’t that
>>> unanimous either.
>>> 
>>> My stand:
>>> 
>>> When the default resolution cutoff provided with the data processing
>>> software in electron density map calculation and refinement delivers
>>> 

Re: [ccp4bb] CCP4BB Digest - 27 Feb 2020 to 28 Feb 2020 (#2020-61)

[dusan turk]

Hi again,

First, I wish to thank everyone for their responses. I hope that no one minds 
that I include them in my response letter to the Editor ?

The idea of citing the Karplus and Diedrichs paper in Science has been 
essentially consumed already in our first response letter, which accompanied 
the submission of the revised manuscript,  and did not work. (Instead of the 
Science citation from 2012 we used a quote from the paper suggested below by 
Karplus and Diederichs, Curr Opin Struct Biol. 2015 Oct; 34: 60–68. )

As Phoebe mentioned, it would be good to use the momentum. My intention of 
writing to the bulletin board was not only to get help with argumentation, but 
also to raise the issue of how to address resolution cutoffs in 
crystallographic data in publications  to avoid such situations in general. I 
also think that the issue is more complicated than the last shell criterion 
with I/Isig > xx, Rmerge < yy, or cc1/2 > zz, or ...

1. Number of reflections in a shell effects the numbers significantly. The 
larger numbers of the shells there are the larger the numbers will be.  The 
number of reflections in a shell depends also on the highest resolution and 
unit cell size. Hence we have a dependance of potential criteria on several 
parameters. 

2. Refinement and data processing programs use different numbers of shells and 
even different ways of calculating shells. REFMAC typically uses 20 equal 
volume sliced shells), PHENIX is more complicated, as far as I understand 
(shell number may depend on the number of TEST set reflections in individual 
shell, shells can be defined according to equal  slicing volume,  some kind of 
log dependency or even linearly according to real space resolution), in MAIN 
there are  20 shells by default, but one can choose any of the mentioned 
slicing rules.

I suggest that we use this discussion to shape up guidelines that can later 
proposed for consideration to the IUCr committee for macromolecules.  I prefer 
soft as opposed to strict borders.  In the end, the structures do not speak for 
themselves, but are a mean to support one or more biologically relevant 
conclusions.

???

best wishes,
dusan turk


> On 29 Feb 2020, at 01:00, CCP4BB automatic digest system 
>  wrote:
> 
> 
> Date:Fri, 28 Feb 2020 16:03:22 +
> From:"Phoebe A. Rice" 
> Subject: Re: What resolution - X-ray diffraction round this time
> 
> Can we get some momentum for the "standard table 1" including TWO numbers - 
> outer limit used in refinement, and nominal resolution based on some standard 
> such as I/sigI =2 (or 3, or whatever the community can agree on)? That would 
> hopefully cut down on all the reviewer complaints of overstated resolution.
> 
> ~~~
> Phoebe A. Rice
> Dept. of Biochem & Mol. Biol. and
>  Committee on Microbiology
> https://voices.uchicago.edu/phoebericelab/
> 
> 
> On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" 
>  wrote:
> 
>Dear colleagues,
> 
>I agree with all the previous responses, it is a pity to throw away
>useful high-resolution data. The problem of high-resolution cutoff
>estimation is also nicely summarized in another paper by Andrew Karplus
>and Kay Diederichs "Assessing and maximizing data quality in
>macromolecular crystallography"
>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ . It is suggested
>using CC1/2 for the selection of the cutoff for data processing (not
>I/sigI or R_whatever). Later on, the decision should be validated
>performing the paired refinement protocol.
> 
>Good luck with the argumentation.
>Martin
> 
> 
>On 2/28/20 11:08 AM, LMB wrote:
>> Ask the referee - (apart from the other suggestions here)
>> 
>> ‘How would removing data Improve my model?”
>> 
>> Sent from my iPad
>> 
>>> On 28 Feb 2020, at 08:22, dusan turk  wrote:
>>> 
>>> Hi,
>>> 
>>> Browsing through the recent discussion on EM data resolution cutoff
>>> it occurred to me that the X-ray diffraction community isn’t that
>>> unanimous either.
>>> 
>>> My stand:
>>> 
>>> When the default resolution cutoff provided with the data processing
>>> software in electron density map calculation and refinement delivers
>>> quality maps noisier than expected and/or too high R-factors I start
>>> adjusting the resolution cutoff by lowering the resolution and trying
>>> alternative space group. Hence, I allow the data processing programs
>>> to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R
>>> sym, R p.i.m. and R r.i.m, …) , unless there are problems.
>>> 
>>> Doing so, I came into a dispute with a referee who shaped his request:
>>> 
>>> "It is well accepted that the criteria for resolution cutoff should
>>> consider both I/SigI and Rmerge for the outer most shell. For data
>>> sets collected at synchrotron sources, the criteria of I/SigI > 5 and
>>> Rmerge <50% can be taken as a good practical reference.”
>>> 
>>> So where do we stand? Which are 

Re: [ccp4bb] CCP4BB Digest - 24 Mar 2019 to 25 Mar 2019 (#2019-91)

[dturk]

Jan,

you my wish to try MAIN as an alternative "http://www-bmb.ijs.si/;. The 
superimposition parameters obtained from either FatCat or MAIN directly are 
directly saved into the form that is used in map rotation and translation. Maps 
do not have to be in a unit cell (it may be simpler though).

The scripts are generated during setup of an interactive session when 
generating NCS operators (in the case the molecules do not contain highly 
identical sequences  FatCat/CE interface has to be used). The scripts can be 
called during non-interactive use too.

If you have any questions or you need additional information to the manual 
please ask. 

best, dusan




Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://stef.ijs.si/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biology
fax:  +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com


> On 26 Mar 2019, at 01:00, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Sun, 24 Mar 2019 21:57:45 -0700
> From:Jan Abendroth 
> Subject: Re: map rotation
> 
> Hi all,
> thanks for the feedback. Suggestions like coot or pymol won't work for us
> well, since we will have to do this with dozens of structures/maps.So, I'd
> rather have this scripted.
> 
> Still running into some issues that I think relate to maprot.
> My understanding is that I first have to create a map covering molecule B
> that I want to map on A. Checking the extend of the map in chimera confirms
> that this worked:
> 
> 
> mapmask \
> 
> mapin 2mol_2mFo-DFc.map \
> 
> xyzin 2mol_B.pdb \
> 
> mapout 2mol_2mFo-DFc_B.map \
> 
> << eof
> 
> border 5
> 
> eof
> 
> 
> Next, I need to rotate/translate the map in maprot. Since in maprot, mapin
> requires a map that covers the unit cell, I use wrkin and 'mode to' as
> below. In this script, the cell and grid values are the same mapdump
> provides me for the map. The rotation and translation are from superpose,
> RMSD of that superposition is 0.5Å.
> 
> 
> maprot  \
> 
> wrkin  2mol_2mFo-DFc_B.map \
> 
> mapout 2mol_2FoFc_rot.map \
> 
> << eof
> 
> CELL xtal 61.0100   142.360068.280090.97.198090.
> 
> GRID xtal 100 228 112
> 
> MODE to
> 
> AVER
> 
> rota euler 152.440   110.24328.112
> 
> TRANS  -42.212 5.510   -57.243
> 
> eof
> 
> 
> The issue now is that the superposed map for the center of molecule A looks
> great. Towards the edges of the molecule it gets weaker, does not match up
> with the molecule or stops entirely. Again, molecule and maps between A and
> B, as visualized in Coot by NCS hopping, are very similar.
> 
> 
> I am still quite puzzled by what is happening. I guess I am missing
> something in maprot. Any input would be appreciated. This is public data,
> so I would be happy to share the data.
> 
> 
> Cheers,
> 
> Jan
> 
> 
> 
> On Wed, Mar 20, 2019 at 9:26 PM Jan Abendroth 
> wrote:
> 
>> Hi all,
>> this should be easy, scripting the rotation of a map.
>> Purpose for this is: Superimpose several structures of the same protein
>> that crystallized in different space groups, and then drag the maps along.
>> As a simple test, I took a dimeric protein and try to superimpose molecule
>> B along with the map on molecule A.
>> 
>> The execution should be straightforward:
>> a) take a map that covers the unit cell (fft),
>> b) generate a mask around molecule B (mapmask),
>> c) apply rotation/translation that I obtain from superimposing molecule B
>> on molecule A.
>> 
>> The issue is that the obtained map covers both molecule A and B (not a big
>> deal), more importantly, it cuts of certain areas on both molecules.
>> Molecule A and B have low RMSDs (0.5Å).
>> 
>> I must be missing something fairly obvious, have not been able to see
>> what. Feedback would be much appreciated. Scripts are below.
>> 
>> Thanks!
>> Jan



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Re: [ccp4bb] : [ccp4bb] SO4 or PO4

[Jim Pflugrath]

Besides the anomalous difference peak which might be similar in height to
the anom diff peak from an intrinsic sulfur found in cysteine or
methionine, also consider hydrogen bonding.

In general, a sulfate will not be donating a hydrogen bond.  A phosphate
probably will.



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Re: [ccp4bb] CCP4BB Digest - 15 Feb 2019 to 16 Feb 2019 (#2019-53)

[Luecke, Hartmut]

Hi!

As suggested below sulfur/phosphorous anomalous difference Fourier density 
would be nice, but you might be able to figure out what's going without 
collecting more data. Have you investigated the direct interaction partners of 
your mystery oxyanion?  Unless you are at extreme pH values, phosphate will 
have at least one proton that is looking for a hydrogen bond acceptor.  In 
contrast, sulfate/sulphate will generally not have a proton to donate (SO4--).  
You might want to inspect the binding sites of sulfate and phosphate binding 
protein, respectively.


My two Kronas, Hudel

Date:Sat, 16 Feb 2019 17:05:17 +0800
From:张士军 <21620150150...@stu.xmu.edu.cn>
Subject: SO4 or PO4

Dear all

I have got a crystal grown at the condition both have ion of SO4 and PO4, 
and the diffraction resolution is very well, but the problem is coming: how to 
tell which is which just from electron density? I think they are exactly same. 
Thanks a lot !!!

Beat Regards

Shijun



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--

Date:Sat, 16 Feb 2019 11:14:07 -0500
From:jlliu20022002 liu 
Subject: Re: SO4 or PO4

How about collect data at sulfur peak. You might see anomalous peak for
sulfur.

Jinyu

On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
> and the diffraction resolution is very well, but the problem is coming: 
how
> to tell which is which just from electron density? I think they are 
exactly
> same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> 
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>



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--

Date:Sat, 16 Feb 2019 11:47:55 -0500
From:Roger Rowlett 
Subject: Re: SO4 or PO4

Two things to look at that could provide a clue:

Examine the anomalous map for some density over the central atom. Sulfur
will often, but not always have significant anomalous density depending on
the wavelength and quality of data set.

Phosphate is normally HPO4= or H2PO4-. Look for phosphate donor to acceptor
hydrogen bonding contacts. Sulfate rarely has donor to acceptor hydrogen
bonding contacts, as it is SO4= at any reasonable pH.

Roger Rowlett

On Sat, Feb 16, 2019, 4:06 AM 张士军 <21620150150...@stu.xmu.edu.cn wrote:

> Dear all
>
> I have got a crystal grown at the condition both have ion of SO4 and PO4,
> and the diffraction resolution is very well, but the problem is coming: 
how
> to tell which is which just from electron density? I think they are 
exactly
> same. Thanks a lot !!!
>
> Beat Regards
>
> Shijun
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> 
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwIFaQ=dzukdOe-KyRBOwGgecHzPA=eBJx8Uo9bg3PQBubUBW3Kw=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY=
>



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--

Date:Sat, 16 Feb 2019 16:54:37 +
From:"david lawson (JIC)" 
Subject: Warning - ccp4 update 7.0.069 breaks ccp4i2 on MacBook running 
Mojave (v 10.14.2)

Hi All,

I installed the latest ccp4 update on my MacBook through the CCP4i2 

Re: [ccp4bb] CCP4BB Digest - 11 Sep 2018 to 12 Sep 2018 (#2018-231)

[Chris Morris - UKRI STFC]

It's 1/e. To some of us, that's a round number.

-Original Message-
From: CCP4 bulletin board  On Behalf Of CCP4BB automatic 
digest system
Sent: 13 September 2018 00:14
To: ccp4bb 
Subject: CCP4BB Digest - 11 Sep 2018 to 12 Sep 2018 (#2018-231)

There is 1 message totaling 48 lines in this issue.

Topics of the day:

  1. D37



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--

Date:Wed, 12 Sep 2018 17:51:58 -0500
From:Murpholino Peligro 
Subject: D37

I just found a paper* where this metric, D37,  is used.

Third page, line #8:
D37 (the radiation dose which reduces the activity to 37% of the control value"

* http://www.jbc.org/content/257/22/13297.full.pdf

The question is why 37? why not 50 or something else?

Thank you.



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--

End of CCP4BB Digest - 11 Sep 2018 to 12 Sep 2018 (#2018-231)
*



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Re: [ccp4bb] [ccp4bb] Oxford University Press

[Eugene Osipov]

AI researchers are boycotting Nature journals:
http://www.sciencemag.org/news/2018/05/why-are-ai-researchers-boycotting-new-nature-journal-and-shunning-others
May be there is something we can in our field?

2018-07-02 10:01 GMT+03:00 George Sheldrick :

> Since neither I nor my university can afford Elsevier journals, I have no
> access to papers published in them. In view of their excessive profits, for
> some years I have not submitted papers to them and have declined all
> requests to referee for them. If everyone did that, they might reconsider
> their approach. I am not an Apple fan either - I use a more reasonably
> priced native Linux laptop - but have to give Apple credit for innovation.
>
> George
>
>
>
> On 07/01/2018 06:57 PM, Patrick Loll wrote:
>
>
> I think what we should do is not publish in journal families where the
> profit is above 10 per cent. Elsevier is the place to start as their profit
> margins are like those of Apple, and of competition there is none.
>
>
> Elsevier: Like Apple, but without the design sense.
>
>
> But seriously, Adrian makes an excellent point. And the large profit
> margins wouldn’t be quite so galling, if only the publishers were able to
> provide competent and helpful administrative support; but in my recent
> experience, not-for-profit scientific society journals are actually
> providing better experiences for reviewers and authors than the big
> commercial ones.
>
> Pat
>
> 
> ---
>
> Patrick J. Loll, Ph. D.
>
> Professor of Biochemistry & Molecular Biology
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St
> .,
> Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pjl...@gmail.com
>
> pj...@drexel.edu
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-33021 or +49-5594-227312
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center of Biotechnology
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com



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Re: [ccp4bb] [ccp4bb] Oxford University Press

[George Sheldrick]

Since neither I nor my university can afford Elsevier journals, I have 
no access to papers published in them. In view of their excessive 
profits, for some years I have not submitted papers to them and have 
declined all requests to referee for them. If everyone did that, they 
might reconsider their approach. I am not an Apple fan either - I use a 
more reasonably priced native Linux laptop - but have to give Apple 
credit for innovation.


George


On 07/01/2018 06:57 PM, Patrick Loll wrote:


I think what we should do is not publish in journal families where 
the profit is above 10 per cent. Elsevier is the place to start as 
their profit margins are like those of Apple, and of competition 
there is none.


Elsevier: Like Apple, but without the design sense.


But seriously, Adrian makes an excellent point. And the large profit 
margins wouldn’t be quite so galling, if only the publishers were able 
to provide competent and helpful administrative support; but in my 
recent experience, not-for-profit scientific society journals are 
actually providing better experiences for reviewers and authors than 
the big commercial ones.


Pat

---

Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St., Mailstop 497

Philadelphia, PA19102-1192USA


(215) 762-7706

pjl...@gmail.com 

pj...@drexel.edu 





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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or +49-5594-227312




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Re: [ccp4bb] [ccp4bb] Oxford University Press

[Robbie Joosten]

There is a way to get some credit for reviewing, which is a good step: 
https://publons.com/home/



You can link it to your ORCID.



Cheers,

Robbie





Sent from my Windows 10 phone




From: CCP4 bulletin board  on behalf of 
graeme.win...@diamond.ac.uk 
Sent: Sunday, July 1, 2018 7:13:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Jacob,

This is a known thing in other circles - see e.g.

https://arxiv.org/abs/1011.6590

"Extending ArXiv.org<http://ArXiv.org> to Achieve Open Peer Review and 
Publishing

Axel Boldt
(Submitted on 23 Nov 2010)
Today's peer review process for scientific articles is unnecessarily opaque and 
offers few incentives to referees. Likewise, the publishing process is 
unnecessarily inefficient and its results are only rarely made freely available 
to the public. Here we outline a comparatively simple extension of 
arXiv.org<http://arXiv.org>, an online preprint archive widely used in the 
mathematical and physical sciences, that addresses both of these problems. 
Under the proposal, editors invite referees to write public and signed reviews 
to be attached to the posted preprints, and then elevate selected articles to 
"published" status.”

Also:

http://blog.scienceopen.com/2016/04/what-if-you-could-peer-review-the-arxiv/

And:

https://www.theguardian.com/science/occams-corner/2015/sep/07/peer-review-preprints-speed-science-journals

(different things)

I think the idea here is that people want to trust the manuscript - having it 
in Acta Cryst D (or whatever else) does give some measure of provenance. I 
suspect we could achieve the same with an open peer review process but it would 
be non-trivial, especially for most of the stuff which ends up in Nature… 
though this does not make it wrong, just hard.

Cheerio Graeme

On 1 Jul 2018, at 04:17, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

I don't fully understand the cynicism in the response, unless it is simply the 
outpouring from years of painstaking review work for no monetary reward in a 
very broken publication system. Everybody I have talked to thinks the system is 
terrible, and various solutions have been proposed. One of these is, believe it 
or not, what I suggested, which is to pay reviewers. It is a huge amount of 
work, if one has a conscience about it, and the number of people with the 
expertise and experience required for this type of work is exceedingly small. 
Further, a real review of a paper takes significantly more than 2 hours of 
work, depending on the type of paper (I think you were joking about 2 h, but 
not totally sure). What really kills me is that the publishing houses are 
making money hand over fist, and this because they know that they can get very 
cooperative scientists (G-d bless them) to do huge amounts of work for free. It 
is really scandalous, and I am not sure why we scientists go along with it. To 
put it bluntly: we are being exploited by the journals; why not do something 
about it? I am sure that the journals will not be overjoyed to release their 
grip on the profits, but that should not stop us.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hughes, 
Jon
Sent: Saturday, June 30, 2018 6:13 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00

Re: [ccp4bb] [ccp4bb] Oxford University Press

[Goldman, Adrian]

I personally don’t think paying reviewers is a necessary solution, though it 
would be nice- for us. The result would just be an increase in journal costs. 

I think what we should do is not publish in journal families where the profit 
is above 10 per cent. Elsevier is the place to start as their profit margins 
are like those of Apple, and of competition there is none. 

Adrian 

Sent from my iPhone

> On 1 Jul 2018, at 05:18, Keller, Jacob  wrote:
> 
> I don't fully understand the cynicism in the response, unless it is simply 
> the outpouring from years of painstaking review work for no monetary reward 
> in a very broken publication system. Everybody I have talked to thinks the 
> system is terrible, and various solutions have been proposed. One of these 
> is, believe it or not, what I suggested, which is to pay reviewers. It is a 
> huge amount of work, if one has a conscience about it, and the number of 
> people with the expertise and experience required for this type of work is 
> exceedingly small. Further, a real review of a paper takes significantly more 
> than 2 hours of work, depending on the type of paper (I think you were joking 
> about 2 h, but not totally sure). What really kills me is that the publishing 
> houses are making money hand over fist, and this because they know that they 
> can get very cooperative scientists (G-d bless them) to do huge amounts of 
> work for free. It is really scandalous, and I am not sure why we scientists 
> go along with it. To put it bluntly: we are being exploited by the journals; 
> why not do something about it? I am sure that the journals will not be 
> overjoyed to release their grip on the profits, but that should not stop us.
> 
> JPK
> 
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> Desk: (571)209-4000 x3159
> Cell: (301)592-7004
> +
> 
> The content of this email is confidential and intended for the recipient 
> specified in message only. It is strictly forbidden to share any part of this 
> message with any third party, without a written consent of the sender. If you 
> received this message by mistake, please reply to this message and follow 
> with its deletion, so that we can ensure such a mistake does not occur in the 
> future.
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hughes, 
> Jon
> Sent: Saturday, June 30, 2018 6:13 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press
> 
> great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
> reasonable starting point for negotiations. if the publishers don't like our 
> price, they can do the reviewing themselves - and after a while no one will 
> bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
> online directly (without wasting our time, for example, still formatting 
> reference lists in the 21st century!). we have them over a barrel. the only 
> problem i see is how to get grants without papers in Nature. anyone have a 
> solution to that one?
> one final aspect is: who gets the money? surely the universities etc. should 
> get it, not us: the taxpayer pays us already. 
> best,
> jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Keller, Jacob
> Gesendet: Samstag, 30. Juni 2018 00:00
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press
> 
> The one I don't get is why not pay reviewers? $1000 per review? If you look 
> at publishers' profit margins, you will see that they can afford it. I 
> actually think the scientific community should go on a "review strike" until 
> reviewers get paid.
> 
> JPK
> 
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> Desk: (571)209-4000 x3159
> Cell: (301)592-7004
> +
> 
> The content of this email is confidential and intended for the recipient 
> specified in message only. It is strictly forbidden to share any part of this 
> message with any third party, without a written consent of the sender. If you 
> received this message by mistake, please reply to this message and follow 
> with its deletion, so that we can ensure such a mistake does not occur in the 
> future.
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr

Re: [ccp4bb] [ccp4bb] Oxford University Press

[graeme.win...@diamond.ac.uk]

Jacob,

This is a known thing in other circles - see e.g.

https://arxiv.org/abs/1011.6590

"Extending ArXiv.org<http://ArXiv.org> to Achieve Open Peer Review and 
Publishing

Axel Boldt
(Submitted on 23 Nov 2010)
Today's peer review process for scientific articles is unnecessarily opaque and 
offers few incentives to referees. Likewise, the publishing process is 
unnecessarily inefficient and its results are only rarely made freely available 
to the public. Here we outline a comparatively simple extension of 
arXiv.org<http://arXiv.org>, an online preprint archive widely used in the 
mathematical and physical sciences, that addresses both of these problems. 
Under the proposal, editors invite referees to write public and signed reviews 
to be attached to the posted preprints, and then elevate selected articles to 
"published" status.”

Also:

http://blog.scienceopen.com/2016/04/what-if-you-could-peer-review-the-arxiv/

And:

https://www.theguardian.com/science/occams-corner/2015/sep/07/peer-review-preprints-speed-science-journals

(different things)

I think the idea here is that people want to trust the manuscript - having it 
in Acta Cryst D (or whatever else) does give some measure of provenance. I 
suspect we could achieve the same with an open peer review process but it would 
be non-trivial, especially for most of the stuff which ends up in Nature… 
though this does not make it wrong, just hard.

Cheerio Graeme

On 1 Jul 2018, at 04:17, Keller, Jacob 
mailto:kell...@janelia.hhmi.org>> wrote:

I don't fully understand the cynicism in the response, unless it is simply the 
outpouring from years of painstaking review work for no monetary reward in a 
very broken publication system. Everybody I have talked to thinks the system is 
terrible, and various solutions have been proposed. One of these is, believe it 
or not, what I suggested, which is to pay reviewers. It is a huge amount of 
work, if one has a conscience about it, and the number of people with the 
expertise and experience required for this type of work is exceedingly small. 
Further, a real review of a paper takes significantly more than 2 hours of 
work, depending on the type of paper (I think you were joking about 2 h, but 
not totally sure). What really kills me is that the publishing houses are 
making money hand over fist, and this because they know that they can get very 
cooperative scientists (G-d bless them) to do huge amounts of work for free. It 
is really scandalous, and I am not sure why we scientists go along with it. To 
put it bluntly: we are being exploited by the journals; why not do something 
about it? I am sure that the journals will not be overjoyed to release their 
grip on the profits, but that should not stop us.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hughes, 
Jon
Sent: Saturday, June 30, 2018 6:13 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

++

Re: [ccp4bb] [ccp4bb] Oxford University Press

[Keller, Jacob]

I don't fully understand the cynicism in the response, unless it is simply the 
outpouring from years of painstaking review work for no monetary reward in a 
very broken publication system. Everybody I have talked to thinks the system is 
terrible, and various solutions have been proposed. One of these is, believe it 
or not, what I suggested, which is to pay reviewers. It is a huge amount of 
work, if one has a conscience about it, and the number of people with the 
expertise and experience required for this type of work is exceedingly small. 
Further, a real review of a paper takes significantly more than 2 hours of 
work, depending on the type of paper (I think you were joking about 2 h, but 
not totally sure). What really kills me is that the publishing houses are 
making money hand over fist, and this because they know that they can get very 
cooperative scientists (G-d bless them) to do huge amounts of work for free. It 
is really scandalous, and I am not sure why we scientists go along with it. To 
put it bluntly: we are being exploited by the journals; why not do something 
about it? I am sure that the journals will not be overjoyed to release their 
grip on the profits, but that should not stop us.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hughes, 
Jon
Sent: Saturday, June 30, 2018 6:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already. 
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we 

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

[Hughes, Jon]

...that some papers get waived through isn't all that uncommon already, 
especially with Nature.
j

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Vellieux 
Frédéric
Gesendet: Samstag, 30. Juni 2018 12:23
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

"how to get grants without papers in Nature. anyone have a solution to that 
one?"
Simple: Once all of us have reviewed enough papers (with the money placed in a 
common pot) we simply buy the Nature Publishing Group. All those having taken 
part get a Nature paper every 4 years to ensure grant money continues to flow 
in.
F.

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Hughes, Jon 
mailto:jon.hug...@bot3.bio.uni-giessen.de>>
Sent: Saturday, June 30, 2018 12:12:50 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime.

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon 
> mailto:jon.hug...@bot3.bio.uni-giessen.de>>
>  wrote:
>
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Betreff: Re: [ccp4bb] Oxford University Press
>
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
>
> Anyway, if people want to read your papers and cannot get them from
> ResearchGate, I'm sure they can find them on another online
> collection, a hub of some sort ;)
>
> Cheers,
> Robbie

[ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

[Hughes, Jon]

sorry about the typing error. 2 x 200 = 400, i know.
j

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Hughes, 
Jon
Gesendet: Samstag, 30. Juni 2018 12:13
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already. 
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
> 
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
> 
> Anyway, if people want to read your papers and cannot get them from 
> ResearchGate, I'm sure they can find them on another online 
> collection, a hub of some sort ;)
> 
> Cheers,
> Robbie
> 
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>> 
>> Agreed, but for 10 years old papers this seems a bit of overkill
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Robbie 
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Were they open access papers? If they were, than OUP is being too 
>> aggressive (IMO), but otherwise it makes sense. I also find the 
>> ResearchGate is rather aggressive in bugging you to upload papers 
>

Re: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

[Vellieux Frédéric]

"how to get grants without papers in Nature. anyone have a solution to that 
one?"

Simple: Once all of us have reviewed enough papers (with the money placed in a 
common pot) we simply buy the Nature Publishing Group. All those having taken 
part get a Nature paper every 4 years to ensure grant money continues to flow 
in.

F.

From: CCP4 bulletin board  on behalf of Hughes, Jon 

Sent: Saturday, June 30, 2018 12:12:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime.

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
>
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
>
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
>
> Anyway, if people want to read your papers and cannot get them from
> ResearchGate, I'm sure they can find them on another online
> collection, a hub of some sort ;)
>
> Cheers,
> Robbie
>
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>>
>> Agreed, but for 10 years old papers this seems a bit of overkill
>>
>>
>>
>> From: CCP4 bulletin board  On Behalf Of Robbie
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>>
>>
>>

[ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

[Hughes, Jon]

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already. 
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
> 
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
> 
> Anyway, if people want to read your papers and cannot get them from 
> ResearchGate, I'm sure they can find them on another online 
> collection, a hub of some sort ;)
> 
> Cheers,
> Robbie
> 
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>> 
>> Agreed, but for 10 years old papers this seems a bit of overkill
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Robbie 
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Were they open access papers? If they were, than OUP is being too 
>> aggressive (IMO), but otherwise it makes sense. I also find the 
>> ResearchGate is rather aggressive in bugging you to upload papers 
>> that are readily available from the publisher. The whole business bit 
>> in scientific publishing is a necessary (?) evil, but I guess if 
>> given the choice one should publish somewhere where you as an author retain 
>> copyright.
>> 
>> 
>> 
>> Cheers,
>&g

Re: [ccp4bb] [ccp4bb] Oxford University Press

[Keller, Jacob]

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
> 
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
> 
> Anyway, if people want to read your papers and cannot get them from 
> ResearchGate, I'm sure they can find them on another online 
> collection, a hub of some sort ;)
> 
> Cheers,
> Robbie
> 
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>> 
>> Agreed, but for 10 years old papers this seems a bit of overkill
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Robbie 
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Were they open access papers? If they were, than OUP is being too 
>> aggressive (IMO), but otherwise it makes sense. I also find the 
>> ResearchGate is rather aggressive in bugging you to upload papers 
>> that are readily available from the publisher. The whole business bit 
>> in scientific publishing is a necessary (?) evil, but I guess if 
>> given the choice one should publish somewhere where you as an author retain 
>> copyright.
>> 
>> 
>> 
>> Cheers,
>> 
>> Robbie
>> 
>> 
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Bernhard Rupp
>> Sent: Friday, June 29, 2018 11:42
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Hi Fellows,
>> 
>> 
>> 
>> just an advisory that Oxford University Press is pretty aggressive in
>> 
>> enforcing copyright - I had to remove 2 Bioinformatics papers
>> 
>> from ResearchGate.
>> 
>> 
>> 
>> Fortunately, authors have choices, too
>> 
>> 
>> 
>> Cheers, BR
>> 
>> --
>> 
>> Bernhard Rupp
>> 
>> http://www.hofkristallamt.org/
>> 
>> b...@hofkristallamt.org
>> 
>> +1 925 209 7429
>> 
&g

Re: [ccp4bb] [ccp4bb] Oxford University Press

[Petr Leiman]

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime. 

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
> 
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
> 
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie 
> Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
> 
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
> 
> Anyway, if people want to read your papers and cannot get them from 
> ResearchGate, I'm sure they can find them on another online collection, a hub 
> of some sort ;)
> 
> Cheers,
> Robbie 
> 
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>> 
>> Agreed, but for 10 years old papers this seems a bit of overkill
>> 
>> 
>> 
>> From: CCP4 bulletin board  On Behalf Of Robbie 
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Were they open access papers? If they were, than OUP is being too 
>> aggressive (IMO), but otherwise it makes sense. I also find the 
>> ResearchGate is rather aggressive in bugging you to upload papers that 
>> are readily available from the publisher. The whole business bit in 
>> scientific publishing is a necessary (?) evil, but I guess if given 
>> the choice one should publish somewhere where you as an author retain 
>> copyright.
>> 
>> 
>> 
>> Cheers,
>> 
>> Robbie
>> 
>> 
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Bernhard Rupp
>> Sent: Friday, June 29, 2018 11:42
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Oxford University Press
>> 
>> 
>> 
>> Hi Fellows,
>> 
>> 
>> 
>> just an advisory that Oxford University Press is pretty aggressive in
>> 
>> enforcing copyright - I had to remove 2 Bioinformatics papers
>> 
>> from ResearchGate.
>> 
>> 
>> 
>> Fortunately, authors have choices, too
>> 
>> 
>> 
>> Cheers, BR
>> 
>> --
>> 
>> Bernhard Rupp
>> 
>> http://www.hofkristallamt.org/
>> 
>> b...@hofkristallamt.org
>> 
>> +1 925 209 7429
>> 
>> +43 676 571 0536
>> 
>> --
>> 
>> Many plausible ideas vanish
>> 
>> at the presence of thought
>> 
>> --
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] CCP4BB Digest - 24 Jun 2018 to 25 Jun 2018 (#2018-154)

[Mateo Seoane Blanco]

Quoting CCP4BB automatic digest system :


There are 6 messages totaling 891 lines in this issue.

Topics of the day:

  1. Postdoctoral position in ABC transporter-mediated  
polysaccharide secretion

  2. refinement papers (3)
  3. I used up all CCP4 projects ... seemingly ... (2)



To unsubscribe from the CCP4BB list, click the following link:
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--

Date:Mon, 25 Jun 2018 00:15:04 +
From:"Zimmer, Jochen (jz3x)" 
Subject: Postdoctoral position in ABC transporter-mediated  
polysaccharide secretion


Dear Colleagues,

I would like to draw your attention to an open postdoctoral position  
in our group. We are interested in how cells synthesize and secrete  
surface polysaccharides to form cell walls and extracellular  
matrices. Specifically, the successful candidate will join our  
efforts to structurally and functionally characterize ABC  
transporter-mediated polysaccharide secretion. The project involves  
crystallographic and cryo electron microscopy techniques combined  
with in vitro reconstitutions of transport processes.


The University of Virginia provides an excellent environment for  
interdisciplinary research in microbiology, infectious diseases, and  
membrane biophysics. UVA maintains state-of-the-art infrastructures  
for structural biology, including NMR and EPR spectroscopy, electron  
microscopy, X-ray crystallography, and super-resolution microscopy.  
Interested candidates are encourage to contact me directly  
(jochen_zim...@virginia.edu).


Sincerely,
Jochen Zimmer


***

Jochen Zimmer, D. Phil.

Associate Professor

University of Virginia

Molecular Physiology & Biol. Physics

480 Ray C. Hunt Dr.

Snyder Bldg. #380

Charlottesville, VA 22908, USA

Phone: 434 243 6506



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--

Date:Mon, 25 Jun 2018 12:21:27 +
From:Careina Edgooms 
Subject: refinement papers

Hello everyone
I am giving talk about refinement and model building. I wonder if  
anyone knows of latest relevant papers on this topic that you could  
suggest for me?thank you

Careina



To unsubscribe from the CCP4BB list, click the following link:

--

Date:Mon, 25 Jun 2018 16:57:35 +0200
From:Misba Ahmad 
Subject: Re: refinement papers

Here are some nice papers:

journals.iucr.org/d/issues/2012/04/00/


Best
Misbha


On Mon, 25 Jun 2018 at 14:26, Careina Edgooms <
02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:


Hello everyone

I am giving talk about refinement and model building. I wonder if anyone
knows of latest relevant papers on this topic that you could suggest for me?
thank you

Careina

--

To unsubscribe from the CCP4BB list, click the following link:
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--

Date:Mon, 25 Jun 2018 17:25:54 +
From:Antonio Ariza 
Subject: I used up all CCP4 projects ... seemingly ...

Hi all and sorry ... (I thought it best to apologise pre-emptively  
for this rather long question).



Ok ... so, I know I should have changed over to CCP4i2 a LNG  
time ago, but a student in my lab had trouble transferring his  
projects from CCP4i to CCP4i2, so I decided to postpone it ... and I  
kept postponing it ever since. I have now run into a problem with  
the old CCP4i gui, which means I might have to change over to CCP4i2.



It seems I have run out of projects!


Over the last 4 years I have created 251 projects. After I created  
the last one and worked on it for a while, I went and revisited an  
older project. Now I can't access the last project I created from  
the gui anymore.



The last project I created would, alphabetically speaking, also be  
the last project in the list that appears when you press the "Change  
Project" button at the top of the gui. However, the list that  
appears seems to only have enough spaces for 250 project names,  
which means it shows the first 250 projects (alphabetically) and the  
last project isn't on it. When I press the "Directories"  
button I can see I did indeed create the project that I'm looking  
for and when I check the computer, all the files for this project  
are in their corresponding directory.



I guess, if I were to create a 252nd project with a title that would  
fall towards 

Re: [ccp4bb] CCP4BB Digest - 13 May 2018 to 14 May 2018 (#2018-119)

[Yaoqi Zhou]

Would you help me to place the following information? Thank you.

Dear CCP4ers,
Looking for collaborators to annotate articles relevant to your research

If you have published any article indexed by PUBMED, we invite you to join the 
RELISH (relevant literature search) consortium, whereby annotating the degree 
of relevance for 60 recommended articles to your paper you will be eligible to 
become one of the co-authors on a high-impact, open-database paper.

Each participant’s task will be as follows. Visit 
https://pubmed.ict.griffith.edu.au/register/, input a recent article indexed by 
PubMed (preferably one which you have authored), and annotate all 60 
recommended articles for their relevance regarding the input article.

For more details, please visit 
http://sparks-lab.org/Call-for-participation3.html

Thank you for your interest.

Yaoqi Zhou

Professor & Research Leader

Institute for Glycomics

Griffith University, Gold Coast Campus

Re: [ccp4bb] [ccp4bb] tNCS problem

[Randy Read]

Hi,

Phaser is pretty robust now if you have 2-fold tNCS (indicated by having only 
one large non-origin peak in the native Patterson map), and recent versions are 
better at dealing with higher order tNCS (i.e. 3 or more copies related by 
multiples of a single translation vector).  However, getting higher order tNCS 
to work properly can take a bit more thought and analysis outside the program, 
and if you're unlucky enough to have 2 or more different independent tNCS 
vectors it's not sophisticated enough to deal with that.

One common problem is that tNCS interferes with proper space group 
identification.  For instance, it can be difficult to tell whether you have a 
crystallographic 2(1) screw axis with a parallel NCS 2-fold, or 
crystallographic 2-fold with parallel NCS screw axis.  Both of these will lead 
to tNCS, but one will be much closer to reality.  Also, tNCS can obscure the 
detection of twinning, and sometimes a crystal has both pseudo-symmetry with 
twinning as well as tNCS.

If you want to send me a Phaser log file (off-list), I might be able to make 
some suggestions about what to consider.

Best wishes,

Randy Read

> On 8 May 2018, at 16:02, 苏纪勇  wrote:
> 
> Dear Herman, I tried phaser. It worked. But there are a lot of crashes in the 
> structure. Meanwhile, R factors could not be lowered. I tried to use P1 to 
> process the data, but I do not know how many monomers in the asymetric unit. 
> Bests, JiYG 
> On 05/08/2018 22:50, herman.schreu...@sanofi.com 
>  wrote:
> Dear JiYG,
>  
> Unless the tNCS has caused processing problems, Phaser should automatically 
> deal with tNCS and I would recommend to just give it a try. If it fails, you 
> could try more sophisticated approaches.
>  
> Best,
> Herman
>  
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ???
> Gesendet: Dienstag, 8. Mai 2018 16:41
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] [ccp4bb] tNCS problem
>  
> Dear all, Recently, I collected a data set of a crystal of a big protein, 
> which contains 1000 amino acids. I processed the data to P2. But the data set 
> has tNCS problem. I want to do molecular replacement. Is there anyone know 
> how to deal with this problem? Thanks, JiYG
>  
>  

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] [ccp4bb] Rmergicide Through Programming

[Phil Evans]

> 

> (2) Rsym has just:
> 
>> R sym value in percent.
> 
> see 
> .
>  To be honest, if that is the official definition it does make me wonder what 
> it is doing in the dictionary at all.
> 
> Regards,
> Peter.
> 


Indeed

Re: [ccp4bb] CCP4BB Digest - 10 Apr 2017 to 11 Apr 2017 (#2017-100)

[Jim Pflugrath]

Let's step back a little bit first:

Do these 3 to 4 diffraction data sets (when kept separate) process nicely
individually and have good Rmeas and other results when scaled separately
from each other?  If so, then do they also have the same unit cell
dimensions?

Jim


 Date:Tue, 11 Apr 2017 10:46:25 +0800

> From:高艺娜 
> Subject: Some problems in data processing
>
> Dear all,
> For my crystal, I have to merge 3-4 sets of diffraction data using HKL2000
> program to meet requirements for data completeness, but the problem is the
> Rmerge value was too high to go on every time.
> Did anyone have met the same problem and how to solve it? or some tips for
> solve this problem？
>
> All comments will be appreciated!
>
>

Re: [ccp4bb] CCP4BB Digest - 5 Apr 2017 to 6 Apr 2017 (#2017-95)

[Massimo Domenico Sammito]

Dear all,
Regarding the job submission in SLURM from CCP4i, I wanted to add that it is 
possible for ARCIMBOLDO jobs to do it directly from the interface, you need to 
specify the path to a configuration file containing the required informations. 
More info on this configuration file are found here:
http://chango.ibmb.csic.es/installation
If you need any help for the configuration you can write back to me anytime. 

Best wishes,

Massimo Sammito

> Il giorno 07 apr 2017, alle ore 01:01, CCP4BB automatic digest system 
>  ha scritto:
> 
> There are 7 messages totaling 992 lines in this issue.
> 
> Topics of the day:
> 
>  1. ccp4/coot on macOSSierra (3)
>  2. How to submit to SLURM from CCP4i
>  3. suggestion on protein crystallization optimization from phase separation
>  4. Post-doc in membrane protein structural biology, Pfizer Inc
>  5. Reminder: Structural biologist in metabolic diseases, SGC University of
> Oxford
> 
> --
> 
> Date:Thu, 6 Apr 2017 08:59:24 +
> From:"POHL, EHMKE" 
> Subject: ccp4/coot on macOSSierra
> 
> Dear ccp4 community,
> 
>   I would appreciate any suggestions how to get the ccp4 interfaces (ccp4 and 
> ccp4i2) and coot running on the new MacBook Pro under macOS Sierra 10.12.3. 
> control. I have already tried different Xquartz version with no success
> 
> thanks so much
> 
> Ehmke
> 
> --
> 
> Date:Thu, 6 Apr 2017 10:52:47 +0100
> From:Nikos Pinotsis 
> Subject: Re: ccp4/coot on macOSSierra
> 
> Hi Ehmke,
> 
> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This 
> set up works for me (including pymol etc)
> 
> good luck
> 
> Nikos
> 
> Dr. Nikos Pinotsis
> Institute of Structural and Molecular Biology
> Department of Biological Sciences, 3rd Floor, R313
> Birkbeck College
> Malet Street
> London WC1E 7HX
> T: +44 (0)207 631 6827
> F: +44 (0)207 631 6803
> M: +44 (0)792 384 3593
> 
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>> Dear ccp4 community,
>> 
>>   I would appreciate any suggestions how to get the ccp4 interfaces 
>> (ccp4 and ccp4i2) and coot running on the new MacBook Pro under macOS 
>> Sierra 10.12.3. control. I have already tried different Xquartz 
>> version with no success
>> 
>> thanks so much
>> 
>> Ehmke
> 
> --
> 
> Date:Thu, 6 Apr 2017 11:56:57 +0200
> From:Didier Spittler 
> Subject: Re: ccp4/coot on macOSSierra
> 
> Hello Nikos,
> 
> I use Zquartz 2.7.9 too and it works fine for me.
> 
> Best,
> 
> Didier
> 
> 2017-04-06 11:52 GMT+02:00 Nikos Pinotsis :
> 
>> Hi Ehmke,
>> 
>> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This
>> set up works for me (including pymol etc)
>> 
>> good luck
>> 
>> Nikos
>> 
>> Dr. Nikos Pinotsis
>> Institute of Structural and Molecular Biology
>> Department of Biological Sciences, 3rd Floor, R313
>> Birkbeck College
>> Malet Street
>> London WC1E 7HX
>> T: +44 (0)207 631 6827 <+44%2020%207631%206827>
>> F: +44 (0)207 631 6803 <+44%2020%207631%206803>
>> M: +44 (0)792 384 3593 <+44%207923%20843593>
>> 
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>> 
>> Dear ccp4 community,
>> 
>>   I would appreciate any suggestions how to get the ccp4 interfaces (ccp4
>> and ccp4i2) and coot running on the new MacBook Pro under macOS Sierra
>> 10.12.3. control. I have already tried different Xquartz version with no
>> success
>> 
>> thanks so much
>> 
>> Ehmke
>> 
>> 
>> 
> 
> 
> -- 
> Didier Spittler, PhD
> Phone number : +33658576481
> 
> --
> 
> Date:Thu, 6 Apr 2017 14:31:35 +0200
> From:Jesper Lykkegaard Karlsen 
> Subject: How to submit to SLURM from CCP4i
> 
> #!/bin/bash
> #
> # Simple script for submitting ccp4i jobs to the SLURM queuing system
> # Hack inspired from the ccp4i_condorsub script by Ronan Keegan
> #
> # Jesper Lykkegaard Karlsen 06/04/2017
> #
> 
> # Takes the ccp4i job com file as input
> infile=$2
> 
> # Get the def file location, name and the job number
> def_file_line=`grep \.def $infile`
> def_file=${def_file_line##*-r}
> def_file_name=${def_file##*/}
> job_number_name=${def_file_name%.*}
> 
> # Define and make scratch dir on remote FS
> CCP4_REM_SCR=$HOME/.ccp4_rem_scr
> if [ ! -d $CCP4_REM_SCR ]; then
>mkdir $CCP4_REM_SCR
> fi
> 
> # Move def_file to CCP4_REM_SRC and define new var
> cp -a $def_file $CCP4_REM_SCR/
> 
> # Get the project name from the def file
> project_line=`grep CCP4I $def_file | grep PROJECT `
> project=${project_line##* }
> 
> # Create the condor submission script
> cat << eof > ${CCP4_REM_SCR}/${job_number_name}_${project}_sbatch.sub
> #!/bin/bash
> #SBATCH -N1
> #SBATCH --share
> #SBATCH -o ${CCP4_REM_SCR}/${job_number_name}_${project}_sbatch.out
> 
> source /etc/profile.d/modules.sh
> module load 

[ccp4bb] AW: [ccp4bb] [ccp4bb] protein precipitation reg

[Hughes, Jon]

yes - really, tris should be the buffer of last resort rather than the 
standard. its only general advantages would seem to be that it's cheap and not 
very toxic. 
j

--
Professor Jon Hughes, BSc, PhD
Institute for Plant Physiology
Justus Liebig University, Giessen
Zeughaus, Rm. 341
Senckenbergstr. 3
D35390 Giessen, Germany.
work phone: (+49/0)6419935430
fax:  (+49/0)6419935429
mobile:   (+49/0)1757929098
email:  jon.hug...@uni-giessen.de
homepage:
http://www.uni-giessen.de/fbz/fb08/Inst/pflphys/pflaphygroups/ag-hughes
Sent without the use of Apple products



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Mark 
Wilson
Gesendet: Mittwoch, 29. März 2017 22:12
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] protein precipitation reg

I heartily concur with Craig.  Tris can be a dangerous buffer for many reasons, 
including those listed below.  In addition, as a primary amine, it can 
complicate work with metalloproteins and has moderate nucleophilicity.  There 
is almost always a better buffer choice than Tris.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu 






On 3/29/17 2:53 PM, "CCP4 bulletin board on behalf of CRAIG A BINGMAN"
<CCP4BB@JISCMAIL.AC.UK on behalf of cabing...@wisc.edu> wrote:

>
>
>
>There are almost always better choices than Tris buffer.
>
>
>Mo Cleland used to call it “Trash” buffer.  He is no longer with us, 
>but today I will happily carry that flag in his honor.
>
>
>Tris may show up in your crystal structure, especially at carbohydrate 
>binding sites.
>Tris may be a surprisingly strong competitive inhibitor in your enzyme 
>assays, especially as above.
>Tris has an absolutely miserably bad change in pKa vs. temperature.  It 
>is larger than -0.03 pKa/dT(C).  It can be a catastrophically bad 
>choice for flash-freezing protein aliquots.
>
>
>If you taken the time and incurred the expense of preparing a 
>macromolecular sample for crystallization studies, and you are worried 
>about the price difference between Tris and HEPES, in my opinion you 
>are absolutely worried about the wrong things.
>
>
>Why are people substantially concerned about the buffering capacity of 
>a buffer for final sample preparation?  You have a purified protein, 
>presumably without substrate present.  Exactly what do you think is 
>generating or absorbing hydrogen ions  in that solution?  Oxidation of 
>reducing agent should be about the only thing that is taxing the 
>buffer.  From the example below, oxidation of 5 mM BME will put some 
>pressure on the buffer, but unfortunately Tris accelerates the 
>oxidation of BME relative,  to, say, HEPES. And surely you aren’t just 
>letting the protein sit and oxidize in the refrigerator? Oh you might 
>be since when you tried to snap freeze it in Tris, it turned into 
>cooked egg white because the pH went to over 10 before it vitrified.
>(http://www.sciencedirect.com/science/article/pii/S0031942200801429)
>
>
>Isn’t the whole point to use a small amount of buffer so you can easily 
>push the pH around in crystallization screens? (At which point the 
>sample is usually in 100+ mM buffer.)
>
>
>On Mar 29, 2017, at 2:03 PM, Hughes, Jon 
><jon.hug...@bot3.bio.uni-giessen.de> wrote:
>
>...it's just a wonderful tradition! there's an interesting description 
>of the history of tris in maniatis
>cheers
>jon
> 
>Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im  Auftrag von 
>David Briggs
>Gesendet: Mittwoch, 29. März 2017 17:53
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: Re: [ccp4bb] protein precipitation reg
> 
>It doesn't cost as much as HEPES, iirc.
>On Wed, 29 Mar 2017, 16:36 Keller, Jacob, <kell...@janelia.hhmi.org>
>wrote:
>
>
>A bit off topic, but I’ve always wondered how TRIS got so popular what 
>with it’s pKa of 8.3—does anyone know?
> 
>JPK
> 
>From: CCP4
> bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger  
>Rowlett
>Sent: Wednesday, March 29, 2017 11:10 AM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] protein precipitation reg
>
>
>
>
> 
>What are you dialyzing against? Your storage solution should typically 
>be buffered away from the pI and contain at least a small amount of 
>kosmotropic salt, e.g. NaCl. Some proteins will require additional 
>stabilizing/solubilizing  agents such as glycerol or reducing agents. 
>FYI, Tris-Cl, pH 7.5 has very little buffer capacity (about 15% of the 
>total concentration in the acid direction). We typically use Tris-Cl pH 
>8.0, which is closer to t

[ccp4bb] AW: [ccp4bb] [ccp4bb] protein precipitation reg

[Hughes, Jon]

yes, "oil of vitriol" is sulphuric acid, "blue vitriol" is copper II sulphate 
as i recall.
j


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von CRAIG A 
BINGMAN
Gesendet: Donnerstag, 30. März 2017 05:52
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] protein precipitation reg

Since I’m in full-on cranky old biochemist mode now, I think that vitriol is an 
old name for sulfuric acid.

> On Mar 29, 2017, at 8:40 PM, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
> 
>> And if we are going to pour scorn and vitriol on Tris, why not mention its 
>> large dpKa/dT of 0.03 pH units/deg ?
> 
> Hah! That's what many people are doing when they make buffers: pouring 
> vitriol (HCl) on TRIS! I prefer to pour concentrated HEPES, and get two 
> buffers without adding any extra Cl-.
> 
> JPK

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[CRAIG A BINGMAN]

Since I’m in full-on cranky old biochemist mode now, I think that vitriol is an 
old name for sulfuric acid.

> On Mar 29, 2017, at 8:40 PM, Keller, Jacob  wrote:
> 
>> And if we are going to pour scorn and vitriol on Tris, why not mention its 
>> large dpKa/dT of 0.03 pH units/deg ?
> 
> Hah! That's what many people are doing when they make buffers: pouring 
> vitriol (HCl) on TRIS! I prefer to pour concentrated HEPES, and get two 
> buffers without adding any extra Cl-.
> 
> JPK

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[Keller, Jacob]

>And if we are going to pour scorn and vitriol on Tris, why not mention its 
>large dpKa/dT of 0.03 pH units/deg ?

Hah! That's what many people are doing when they make buffers: pouring vitriol 
(HCl) on TRIS! I prefer to pour concentrated HEPES, and get two buffers without 
adding any extra Cl-.

JPK

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[Janet Newman]

Just to point out that whatever buffer you purify your protein into is possibly 
not the one that will keep your protein happiest.  We had the opportunity of 
testing about 250 proteins in DSF against 26 different buffer / salt 
combinations (in triplicate, with lots of controls) and found out that about 
1/3 of the time the protein was significantly (4C or more) stable in some other 
buffer system than the one it was in.
Ristic, M., Rosa, N., Seabrook, S.A., Newman, J., 2015. Formulation screening 
by differential scanning fluorimetry: how often does it work? Acta 
Crystallographica Section F Structural Biology Communications 71, 1359–1364. 
doi:10.1107/S2053230X15012662

And if we are going to pour scorn and vitriol on Tris, why not mention its 
large dpKa/dT of 0.03 pH units/deg ?

Cheers, Janet

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CRAIG A 
BINGMAN
Sent: Thursday, 30 March 2017 8:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] protein precipitation reg


> On Mar 29, 2017, at 4:15 PM, Chun Luo <c...@accelagen.com> wrote:
> 
> In addition to price, the prevalence of Ni purification may be another reason 
> for Tris popularity. Some His-tagged constructs don't bind to Ni well in 
> HEPES. I wonder if anyone has similar experience or comments. —Chun

No, I have not specifically noted that before.

Additionally, why would you use a positively charged buffer on a weak cation 
exchange resin?  The Ni affinity resins, in addition to their noteworthy 
affinity for various metals, are also weak cation exchange resins.  Binding a 
positively charged buffer to a negatively charged column material can cause pH 
effects that you probably weren’t expecting.

Tris may have some uses.  But using it in a mobile phase with Ni affinity 
columns or as a final sample buffer aren’t the best cases for choosing Tris.  I 
understand it is widely used in aquaculture applications where they are 
treating tens of thousands of gallons of water, and price of the buffer 
substance is an actual consideration.

Craig

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[CRAIG A BINGMAN]

> On Mar 29, 2017, at 4:15 PM, Chun Luo  wrote:
> 
> In addition to price, the prevalence of Ni purification may be another reason 
> for Tris popularity. Some His-tagged constructs don't bind to Ni well in 
> HEPES. I wonder if anyone has similar experience or comments. —Chun

No, I have not specifically noted that before.

Additionally, why would you use a positively charged buffer on a weak cation 
exchange resin?  The Ni affinity resins, in addition to their noteworthy 
affinity for various metals, are also weak cation exchange resins.  Binding a 
positively charged buffer to a negatively charged column material can cause pH 
effects that you probably weren’t expecting.

Tris may have some uses.  But using it in a mobile phase with Ni affinity 
columns or as a final sample buffer aren’t the best cases for choosing Tris.  I 
understand it is widely used in aquaculture applications where they are 
treating tens of thousands of gallons of water, and price of the buffer 
substance is an actual consideration.

Craig

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[Chun Luo]

In addition to price, the prevalence of Ni purification may be another reason 
for Tris popularity. Some His-tagged constructs don't bind to Ni well in HEPES. 
I wonder if anyone has similar experience or comments. --Chun

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark 
Wilson
Sent: Wednesday, March 29, 2017 1:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] protein precipitation reg

I heartily concur with Craig.  Tris can be a dangerous buffer for many reasons, 
including those listed below.  In addition, as a primary amine, it can 
complicate work with metalloproteins and has moderate nucleophilicity.  There 
is almost always a better buffer choice than Tris.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu 






On 3/29/17 2:53 PM, "CCP4 bulletin board on behalf of CRAIG A BINGMAN"
<CCP4BB@JISCMAIL.AC.UK on behalf of cabing...@wisc.edu> wrote:

>
>
>
>There are almost always better choices than Tris buffer.
>
>
>Mo Cleland used to call it “Trash” buffer.  He is no longer with us, 
>but today I will happily carry that flag in his honor.
>
>
>Tris may show up in your crystal structure, especially at carbohydrate 
>binding sites.
>Tris may be a surprisingly strong competitive inhibitor in your enzyme 
>assays, especially as above.
>Tris has an absolutely miserably bad change in pKa vs. temperature.  It 
>is larger than -0.03 pKa/dT(C).  It can be a catastrophically bad 
>choice for flash-freezing protein aliquots.
>
>
>If you taken the time and incurred the expense of preparing a 
>macromolecular sample for crystallization studies, and you are worried 
>about the price difference between Tris and HEPES, in my opinion you 
>are absolutely worried about the wrong things.
>
>
>Why are people substantially concerned about the buffering capacity of 
>a buffer for final sample preparation?  You have a purified protein, 
>presumably without substrate present.  Exactly what do you think is 
>generating or absorbing hydrogen ions  in that solution?  Oxidation of 
>reducing agent should be about the only thing that is taxing the 
>buffer.  From the example below, oxidation of 5 mM BME will put some 
>pressure on the buffer, but unfortunately Tris accelerates the 
>oxidation of BME relative,  to, say, HEPES. And surely you aren’t just 
>letting the protein sit and oxidize in the refrigerator? Oh you might 
>be since when you tried to snap freeze it in Tris, it turned into 
>cooked egg white because the pH went to over 10 before it vitrified.
>(http://www.sciencedirect.com/science/article/pii/S0031942200801429)
>
>
>Isn’t the whole point to use a small amount of buffer so you can easily 
>push the pH around in crystallization screens? (At which point the 
>sample is usually in 100+ mM buffer.)
>
>
>On Mar 29, 2017, at 2:03 PM, Hughes, Jon 
><jon.hug...@bot3.bio.uni-giessen.de> wrote:
>
>...it's just a wonderful tradition! there's an interesting description 
>of the history of tris in maniatis
>cheers
>jon
> 
>Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im  Auftrag von 
>David Briggs
>Gesendet: Mittwoch, 29. März 2017 17:53
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: Re: [ccp4bb] protein precipitation reg
> 
>It doesn't cost as much as HEPES, iirc.
>On Wed, 29 Mar 2017, 16:36 Keller, Jacob, <kell...@janelia.hhmi.org>
>wrote:
>
>
>A bit off topic, but I’ve always wondered how TRIS got so popular what 
>with it’s pKa of 8.3—does anyone know?
> 
>JPK
> 
>From: CCP4
> bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger  
>Rowlett
>Sent: Wednesday, March 29, 2017 11:10 AM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] protein precipitation reg
>
>
>
>
> 
>What are you dialyzing against? Your storage solution should typically 
>be buffered away from the pI and contain at least a small amount of 
>kosmotropic salt, e.g. NaCl. Some proteins will require additional 
>stabilizing/solubilizing  agents such as glycerol or reducing agents. 
>FYI, Tris-Cl, pH 7.5 has very little buffer capacity (about 15% of the 
>total concentration in the acid direction). We typically use Tris-Cl pH 
>8.0, which is closer to the Tris pKa and has good buffer capacity for  
>both acid and base. For pH 7.5 we would typically use HEPES as the 
>storage buffer.
>
>___
>Roger S. Rowlett
>Gordon & Dorothy Kline Professor
>Department of Chemistry
>Colgate University
>13 Oak Drive
>Hamilton, NY 13346
>
>tel: (315)-228-7245
>ofc: (315

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[Mark Wilson]

I heartily concur with Craig.  Tris can be a dangerous buffer for many
reasons, including those listed below.  In addition, as a primary amine,
it can complicate work with metalloproteins and has moderate
nucleophilicity.  There is almost always a better buffer choice than Tris.
Best regards,
Mark

Mark A. Wilson
Associate Professor
Department of Biochemistry/Redox Biology Center
University of Nebraska
N118 Beadle Center
1901 Vine Street
Lincoln, NE 68588
(402) 472-3626
mwilso...@unl.edu 






On 3/29/17 2:53 PM, "CCP4 bulletin board on behalf of CRAIG A BINGMAN"
 wrote:

>
>
>
>There are almost always better choices than Tris buffer.
>
>
>Mo Cleland used to call it “Trash” buffer.  He is no longer with us, but
>today I will happily carry that flag in his honor.
>
>
>Tris may show up in your crystal structure, especially at carbohydrate
>binding sites.
>Tris may be a surprisingly strong competitive inhibitor in your enzyme
>assays, especially as above.
>Tris has an absolutely miserably bad change in pKa vs. temperature.  It
>is larger than -0.03 pKa/dT(C).  It can be a catastrophically bad choice
>for flash-freezing protein aliquots.
>
>
>If you taken the time and incurred the expense of preparing a
>macromolecular sample for crystallization studies, and you are worried
>about the price difference between Tris and HEPES, in my opinion you are
>absolutely worried about the wrong things.
>
>
>Why are people substantially concerned about the buffering capacity of a
>buffer for final sample preparation?  You have a purified protein,
>presumably without substrate present.  Exactly what do you think is
>generating or absorbing hydrogen ions
> in that solution?  Oxidation of reducing agent should be about the only
>thing that is taxing the buffer.  From the example below, oxidation of 5
>mM BME will put some pressure on the buffer, but unfortunately Tris
>accelerates the oxidation of BME relative,
> to, say, HEPES. And surely you aren’t just letting the protein sit and
>oxidize in the refrigerator? Oh you might be since when you tried to snap
>freeze it in Tris, it turned into cooked egg white because the pH went to
>over 10 before it vitrified.
>(http://www.sciencedirect.com/science/article/pii/S0031942200801429)
>
>
>Isn’t the whole point to use a small amount of buffer so you can easily
>push the pH around in crystallization screens? (At which point the sample
>is usually in 100+ mM buffer.)
>
>
>On Mar 29, 2017, at 2:03 PM, Hughes, Jon
> wrote:
>
>...it's just a wonderful tradition! there's an interesting description of
>the history of tris in maniatis
>cheers
>jon
> 
>Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im
> Auftrag von David Briggs
>Gesendet: Mittwoch, 29. März 2017 17:53
>An: CCP4BB@JISCMAIL.AC.UK
>Betreff: Re: [ccp4bb] protein precipitation reg
> 
>It doesn't cost as much as HEPES, iirc.
>On Wed, 29 Mar 2017, 16:36 Keller, Jacob, 
>wrote:
>
>
>A bit off topic, but I’ve always wondered how TRIS got so popular what
>with it’s pKa of 8.3—does anyone know?
> 
>JPK
> 
>From: CCP4
> bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger
> Rowlett
>Sent: Wednesday, March 29, 2017 11:10 AM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: Re: [ccp4bb] protein precipitation reg
>
>
>
>
> 
>What are you dialyzing against? Your storage solution should typically be
>buffered away from the pI and contain at least a small amount of
>kosmotropic salt, e.g. NaCl. Some proteins will require additional
>stabilizing/solubilizing
> agents such as glycerol or reducing agents. FYI, Tris-Cl, pH 7.5 has
>very little buffer capacity (about 15% of the total concentration in the
>acid direction). We typically use Tris-Cl pH 8.0, which is closer to the
>Tris pKa and has good buffer capacity for
> both acid and base. For pH 7.5 we would typically use HEPES as the
>storage buffer.
>
>___
>Roger S. Rowlett
>Gordon & Dorothy Kline Professor
>Department of Chemistry
>Colgate University
>13 Oak Drive
>Hamilton, NY 13346
>
>tel: (315)-228-7245
>ofc: (315)-228-7395
>fax: (315)-228-7935
>email: rrowl...@colgate.edu
>On 3/29/2017 9:38 AM, Akilandeswari Gopalan wrote:
>
>
>Dear all,
>I am a PhD student doing structural studies on a few proteins from
>Mycobacterium tuberculosis. The gene encoding the proteins I work on are
>cloned into pet22b with c terminal His tag. the proteins are expressing
>well. upon purification
> I am getting good yield of protein but during dialysis, the proteins
>precipitate. Kindly suggest some solutions to avoid aggregation. pI of
>one protein is 9.7 and that of the other is 5.6
>
>I am using 25mM Tris pH 7.5 and 100 mM NaCl buffer with 5mM
>beta-mercaptoethanol and 0.5% triton x 100 for lysis, the same buffer
>with 20-30mM imidazole for washing and 300mM imidazole for eluting the
>proteins.
>
> 
>
>Thank you
>
>Regards
>
>Akila  
>
> 
>
>--

Re: [ccp4bb] [ccp4bb] protein precipitation reg

[CRAIG A BINGMAN]

There are almost always better choices than Tris buffer.

Mo Cleland used to call it “Trash” buffer.  He is no longer with us, but today 
I will happily carry that flag in his honor.

Tris may show up in your crystal structure, especially at carbohydrate binding 
sites.
Tris may be a surprisingly strong competitive inhibitor in your enzyme assays, 
especially as above.
Tris has an absolutely miserably bad change in pKa vs. temperature.  It is 
larger than -0.03 pKa/dT(C).  It can be a catastrophically bad choice for 
flash-freezing protein aliquots.

If you taken the time and incurred the expense of preparing a macromolecular 
sample for crystallization studies, and you are worried about the price 
difference between Tris and HEPES, in my opinion you are absolutely worried 
about the wrong things.

Why are people substantially concerned about the buffering capacity of a buffer 
for final sample preparation?  You have a purified protein, presumably without 
substrate present.  Exactly what do you think is generating or absorbing 
hydrogen ions in that solution?  Oxidation of reducing agent should be about 
the only thing that is taxing the buffer.  From the example below, oxidation of 
5 mM BME will put some pressure on the buffer, but unfortunately Tris 
accelerates the oxidation of BME relative, to, say, HEPES. And surely you 
aren’t just letting the protein sit and oxidize in the refrigerator? Oh you 
might be since when you tried to snap freeze it in Tris, it turned into cooked 
egg white because the pH went to over 10 before it vitrified.  
(http://www.sciencedirect.com/science/article/pii/S0031942200801429)

Isn’t the whole point to use a small amount of buffer so you can easily push 
the pH around in crystallization screens? (At which point the sample is usually 
in 100+ mM buffer.)

On Mar 29, 2017, at 2:03 PM, Hughes, Jon 
> 
wrote:

...it's just a wonderful tradition! there's an interesting description of the 
history of tris in maniatis
cheers
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von David 
Briggs
Gesendet: Mittwoch, 29. März 2017 17:53
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] protein precipitation reg

It doesn't cost as much as HEPES, iirc.
On Wed, 29 Mar 2017, 16:36 Keller, Jacob, 
> wrote:
A bit off topic, but I’ve always wondered how TRIS got so popular what with 
it’s pKa of 8.3—does anyone know?

JPK

From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger 
Rowlett
Sent: Wednesday, March 29, 2017 11:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein precipitation reg

What are you dialyzing against? Your storage solution should typically be 
buffered away from the pI and contain at least a small amount of kosmotropic 
salt, e.g. NaCl. Some proteins will require additional stabilizing/solubilizing 
agents such as glycerol or reducing agents. FYI, Tris-Cl, pH 7.5 has very 
little buffer capacity (about 15% of the total concentration in the acid 
direction). We typically use Tris-Cl pH 8.0, which is closer to the Tris pKa 
and has good buffer capacity for both acid and base. For pH 7.5 we would 
typically use HEPES as the storage buffer.

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 3/29/2017 9:38 AM, Akilandeswari Gopalan wrote:
Dear all,
I am a PhD student doing structural studies on a few proteins from 
Mycobacterium tuberculosis. The gene encoding the proteins I work on are cloned 
into pet22b with c terminal His tag. the proteins are expressing well. upon 
purification I am getting good yield of protein but during dialysis, the 
proteins precipitate. Kindly suggest some solutions to avoid aggregation. pI of 
one protein is 9.7 and that of the other is 5.6
I am using 25mM Tris pH 7.5 and 100 mM NaCl buffer with 5mM 
beta-mercaptoethanol and 0.5% triton x 100 for lysis, the same buffer with 
20-30mM imidazole for washing and 300mM imidazole for eluting the proteins.

Thank you
Regards
Akila

--
Akilandeswari G

--


Fehler! Es wurde kein Dateiname angegeben.




David Briggs PhD
Fehler! Es wurde kein Dateiname 
angegeben.about.me/david_briggs

Re: [ccp4bb] CCP4BB Digest - 23 Mar 2017 to 24 Mar 2017 (#2017-83)

[Dusan Turk]

Dear Alex,

try MAIN "http://www-bmb.ijs.si/;

it has a two way interface to Ramachandran plot, you can either display 
“HIS_RAMA” of individual clicked residues in displayed 3D  model and also the 
other way around, you can click on residues in Ramachandran plot and center on 
the residue in 3D model.

If you need some help to on how this works  do not hesitate to contact me.

regards,
dusan
 
> On 25 Mar 2017, at 01:00, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Thu, 23 Mar 2017 20:39:46 -0700
> From:Alex Lee 
> Subject: software or tool for Individual residue in a Ramachandran plot graph?
> 
> Dear All,
> 
> Is there a tool or software which can give Ramachandran information of
> individual residues in a plot?
> 
> I used Coot to check for Ramachandran plots, but it shows all the residues
> in a coordinate I put in Coot, not individual one. I also use "residue
> info" in coot, it tells Ramachandran "phi psi" angles of individual
> residue, but it does not show it in a plot, only numbers.
> 
> Thanks ahead for any input.
> 

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[pselvam]

Dear All,
thanks for your replies.  I tend to believe that it could be ATP some 
how copurified with the protein. Refinement with ATP, ADP+acetate, did 
not vary too much in the B factors. The main concern is, only one xtal 
was observed at this state  ( mimicked like a ATP bound state and 
changed conformation and space group). All other xtals (around 10 xtals 
were measured) from this plate did not have this change.So it was little 
tough to understand that only this xtal has ATP instead of ADP. We were 
not able to reproduce xtals of similar space group with similar setup 
(with ADP). After tremendous  trials we could grow one xtal with ATP 
which has the P212121 space group and all the observed changes. Is any 
one observed ATP mimicking by compounds other than aluminium/berillyium 
Fluoride?



Thanks
Saravanan

Dear All,
Sorry for the little bit off topic. Is there a possibility for covalent
bond formation between beta phosphate of ADP and acetate molecule both
are coordinated by divalent metal ions? I am working on a Kinase
structure  which was crystallized with ADP and in presence of 1M sodium
acetate. We observed additional density around ADP that fits perfectly
like a gamma phosphate , mimicking like ATP bound state, surrounded and
coordinated by two metal ions(resolution is 1.4A). There is a change in
space group (from I212121 to P212121 ) and further important
conformation changes are observed around ATP binding pocket and distant
region. This is the only xtal we obtained in this space group, and all
other xtals(measured 10 xtals)  from the same plate belong to I212121.

  


Thanks your help and time!

Saravanan
Replies:

Hello Saravanan

At 1.4 Angstrom resolution wouldn't that suggest that you've somehow got 
ATP in there ?  I don't think I understand the other option - were you 
proposing a ADP-O-C(O)2 arrangement to explain the density ?  Surely 
that has a rather different shape, considerably different scattering 
power at the center of the terminal group (C vs P) and probably 
different X-O bond lengths.  All of these should show in the density 
maps at 1.4 Å, although the bond length issue could be quite subtle.


Phil Jeffrey
Princeton

Perhaps it is ATP?

Mark J van Raaij


Remember that 2xADP can disproportionate into ATP + AMP


Hi Saravanan

It sounds to me like you have ATP there, even though you added ADP. Is 
your kinase an inactive mutant? I know kinases can bring nucleotides 
along for the ride during purification.


Regards
Christine



--
Dr. Saravanan Panneerselvam PhD
P11 Beamline Scientist
HASYLAB, DESY
Building 25F, Room 360
Notkestrasse, 85
22607, Hamburg
GERMANY
Phone : 0049 40 8998 2692
Mobile:  0049 40 8998 92692
saravananpann...@gmail.com
saravanan.panneersel...@desy.de

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

[Ethan Merritt]

On Thursday, 26 January 2017 11:03:12 PM Claire Smith wrote:
> Hello,
> 
> I would like to ask a question related to a recent thread regarding
> bad/missing density.
> 
> I have used SAD to solve the structure of a protein at about 2.6Å
> resolution. Phenix build a good portion of it (about 50%) and the density
> in this region is good. However, we cannot see ther rest 50%.  Rfree is
> currently at 32%.  No twinning is suggested.
> 
> How can we "find" the missing 50%? We have tried MR-SAD with no significant
> improvement. We know the missing mass is there because we ran the crystals
> on a  gel, and the protein is intact.
> 
> I know with MR sometimes the space group can make a difference, but with
> experimental phasing (SAD),  if the space group were incorrectly
> identified, would we have gotten a solution to the Se substructure? This
> seems correct because the visible 50% of the protein make total sense. So,
> since we have a correct substructure, can I conclude with confidence that
> the space group is correctly identified?

>From your description it sounds unlikely that the unit cell is correct but
the space group is wrong.   However the symptoms do match a possible
missed supercell, such that you collected and refined data from only 
a subset of the true unique data.

I will try to describe this in words but a picture would be so much easier...
I will try ascii art.  Please view in a fixed spacing font.
Suppose the true cell looks like this:
---
| AAA|  AAA  BBB  |
| B  |  BBBB  |
| AAA   BBB  |  AAA   |
---

I.e. suppose you have pseudo-translational NCS such that domain A
superimposes perfectly on itself but domain B does not.
If you incorrectly index that cell edge as being only 1/2 its true length,
you measure only half of the true data but it refines nicely to 
describe a fully-occupied A and a mess in the region where B should be.
(superimposed 1/2 intensity ghosts made noisier by the missing data).

Yes I've hit this in real life, with an even messier case of cell-edge
tripling rather than doubling.
If you want to pursue this possibility, you should go back to the
diffraction images and look really hard for weak spots in between the
indexed spots.

good luck,

Ethan

 
> Of course, it could be that the missing bit is very flexible and does not
> scatter coherently, but then, wouldn't we expect a lower Rfree?

An Rfree of 0.32 for 2.6A refinement doesn't sound that bad.

 
> Thanks so much!
> 
> Claire
> 

-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] CCP4BB Digest - 24 Jan 2017 to 25 Jan 2017 (#2017-26)

[Claire Smith]

Hello,

I would like to ask a question related to a recent thread regarding
bad/missing density.

I have used SAD to solve the structure of a protein at about 2.6Å
resolution. Phenix build a good portion of it (about 50%) and the density
in this region is good. However, we cannot see ther rest 50%.  Rfree is
currently at 32%.  No twinning is suggested.

How can we "find" the missing 50%? We have tried MR-SAD with no significant
improvement. We know the missing mass is there because we ran the crystals
on a  gel, and the protein is intact.

I know with MR sometimes the space group can make a difference, but with
experimental phasing (SAD),  if the space group were incorrectly
identified, would we have gotten a solution to the Se substructure? This
seems correct because the visible 50% of the protein make total sense. So,
since we have a correct substructure, can I conclude with confidence that
the space group is correctly identified?

Of course, it could be that the missing bit is very flexible and does not
scatter coherently, but then, wouldn't we expect a lower Rfree?

Thanks so much!

Claire






On Wed, Jan 25, 2017 at 7:00 PM, CCP4BB automatic digest system <
lists...@jiscmail.ac.uk> wrote:

> There are 13 messages totaling 4586 lines in this issue.
>
> Topics of the day:
>
>   1. add ligand solution onto drop directly (2)
>   2. Bad density for chains (3)
>   3. Unknown electron density blob (2)
>   4. Macromolecular Crystallography School MCS2017 Madrid
>   5. explain "comfortable"
>   6. Unknown electron density blob, pdb convention for partially ordered
>  ligands (3)
>   7. PhD Presidential fellowship to study the Structure and function of
> CRISPR
>  systems
>
> --
>
> Date:Wed, 25 Jan 2017 03:23:18 +0100
> From:Markus Heckmann 
> Subject: add ligand solution onto drop directly
>
> Dear all,
> I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the
> drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of
> dissolving it in precipitant solution and transferring the crystal to this
> ligand containing precipitant solution. The crystals survive this as I add
> the ligand solution to the edge of the drop and gently mix the two
> solutions. Since I collected my datasets I wonder if it is OK?
>
> Many thanks,
> Markus
>
> --
>
> Date:Tue, 24 Jan 2017 19:15:43 -0800
> From:Bernhard Rupp 
> Subject: Re: add ligand solution onto drop directly
>
> The truth is in the map. Ergo, zap it and rationalize why it worked or not
> later.
>
>
>
> Cheers, BR
>
>
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Markus Heckmann
> Sent: Tuesday, January 24, 2017 6:23 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] add ligand solution onto drop directly
>
>
>
> Dear all,
>
> I wondered if it is OK to pipette ligand soln (X-CoA) *directly* to the
> drop with crystal (1:1 ratio of protein:precipitant 2µl) instead of
> dissolving it in precipitant solution and transferring the crystal to this
> ligand containing precipitant solution. The crystals survive this as I add
> the ligand solution to the edge of the drop and gently mix the two
> solutions. Since I collected my datasets I wonder if it is OK?
>
> Many thanks,
>
> Markus
>
> --
>
> Date:Wed, 25 Jan 2017 10:12:55 +0530
> From:Pooja Kesari 
> Subject: Bad density for chains
>
> Dear All,
>
> I have a 2.6 A resolution structure having four chains in an asymmetric
> unit.
> The chain A and B have density for almost all residues however we don't
> have proper residue density in chain C and D.What can be tried to build
> chain C and D ?
>
>
>
> Many Thanks
> Pooja
>
> --
>
> Date:Tue, 24 Jan 2017 21:02:40 -0800
> From:Debanu 
> Subject: Re: Bad density for chains
>
> Hi Pooja,
>
> Are you positive you have the correct space group and there are no other
> issues like twinning, etc?
>
> If sure, did you define NCS groups in refinement? TLS refinement? Try
> different refinement programs?
>
> How big is the molecule? Was it solved by MR or experimental phasing?
>
> You can try superimposing A/B on C/D and refinement with tight NCS then
> adjust NCS restraints during model adjustments based on local differences
> or also see if phenix autobuild helps.
>
> Best,
> Debanu
> --
> Debanu Das
> Accelero Biostructures
>
>
> > On Jan 24, 2017, at 8:42 PM, Pooja Kesari  wrote:
> >
> > Dear All,
> >
> > I have a 2.6 A resolution structure having four chains in an asymmetric
> unit.
> > The chain A and B have density for almost all residues however we don't
> have proper residue density in chain C and D.What can be tried to build
> chain C and D ?
> >
> >
> >
> > Many Thanks
> > Pooja
>
> --
>
> 

Re: [ccp4bb] CCP4BB Digest - 18 Jan 2017 to 19 Jan 2017 (#2017-20)

[Jiang Xu]

Hi, everyone,
 I think I found the cause and solution.
 It was due to the project folder of CCP4i,which was set by me to E:/***/**
p reviously, based on which imosflm automatically set its processing folder
also as E:/***/. Because disk E: used to be the flash disk on my computer,
when I unplug the flash disk, the software cannot find the disk then it
will report the error. When I change the project folder in CCP4i to
D:/***/**, which was present on my computer, the problem was solved.
 Best!
Jiang

On Thu, Jan 19, 2017 at 4:00 PM, CCP4BB automatic digest system <
lists...@jiscmail.ac.uk> wrote:

> There are 23 messages totaling 6640 lines in this issue.
>
> Topics of the day:
>
>   1. on space group (2)
>   2. error in startup script
>   3. AW: [ccp4bb] on space group
>   4. *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error in
> startup
>  script
>   5. Call for MX beamtime proposals at HZB, BESSY II, deadline March 01,
> 2017
>   6. Off-topic, protein in dye-front (ion front?) on native-PAGE (5)
>   7. 6th Edition of the ISBC2017
>   8. Cryosystems series 600
>   9. Unique postdoctoral research opportunity in Tromsø, Norway
>  10. PhD fellowships in Spain
>  11. Anisotropy and temperature (4)
>  12. CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) (3)
>  13. Joint Postdoctoral Position in the Grishin and Chook Labs at UT
>  Southwestern
>
> --
>
> Date:Thu, 19 Jan 2017 02:33:14 +
> From:Smith Lee 
> Subject: on space group
>
>
> Dear All,
> In the literature, somebody call space group P65 crystal as  "six fold
> screw axis crystal packing", then I would not make any mistake if I call
> P64 space group crystal also as  "six fold screw axis crystal packing",am I
> right?
> I am looking forward to getting a reply from you.
>
> --
>
> Date:Wed, 18 Jan 2017 19:40:30 -0800
> From:Jiang Xu 
> Subject: error in startup script
>
> Hi, Mr/Ms,
>I am a user of CCP4i. I recently discovered that imosflm cannot be used
> on my win7. the error message is shown below.
>[image: Inline image 1]
>   However, when I go to 'bin' folder and double click the imosflm.bat, the
> program can be start up successfully. I don't know what's the problem.
> Thank you!
> Best!
> Jiang Xu
> Department of Molecular and Computational Biology
> University of Southern California
>
> --
>
> Date:Thu, 19 Jan 2017 05:22:24 +
> From:Smith Lee 
> Subject: Re: on space group
>
> Dear All,
> Here may I make my question much clear? For the space group P 65 crystal,
> it seems we can call it "6-fold packing of subunits around a screw axis in
> the crystal". Then for the space group P 64 crystal, can it also be called
> "6-fold packing of subunits around a screw axis in the crystal"?
> Smith
>
> On Thursday, January 19, 2017 11:50 AM, Ethan Merritt <
> merr...@u.washington.edu> wrote:
>
>
>  On Thursday, 19 January 2017 02:33:14 AM you wrote:
> >
> > Dear All,
> > In the literature, somebody call space group P65 crystal as  "six fold
> screw axis crystal packing", then I would not make any mistake if I call
> P64 space group crystal also as  "six fold screw axis crystal packing",am I
> right?
> > I am looking forward to getting a reply from you.
> > Smith
>
> "six-fold screw axis" refers to the symmetry.
>
> "crystal packing" refers to the molecule-to-molecule contacts regardless
> of symmetry.
>
> So no, I don't think "six fold screw axis crystal packing" makes any sense.
>
> --
> Ethan A Merritt, Dept of Biochemistry
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,  University of Washington, Seattle 98195-7742
>
>
> --
>
> Date:Thu, 19 Jan 2017 08:47:52 +
> From:herman.schreu...@sanofi.com
> Subject: AW: [ccp4bb] on space group
>
> Dear Smith,
>
> I think your question was clear, and the answer you got was clear as well.
>
> However, I think the question you asked was not the right question. You
> want to use a particular phrase to describe your crystal packing and you
> want the CCP4BB to endorse this. When the answer was negative, you asked
> again the same question.
>
> The real question, in my eyes, is “What is the best way to describe my P65
> crystal packing” since I guess you want to use this in your paper. Here I
> would use something like “in the crystal, the subunits are related by a
> 6-fold screw axis”. To be more precise, you could even mention a 65-screw
> axis. Other board members may even have better descriptions.
>
> By the way, 61, 62, 63, 64 and 65 axes are all 6-fold screw axes, but of
> different types.
>
> Best,
> Herman
>
>
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Smith Lee
> Gesendet: Donnerstag, 19. Januar 2017 06:22
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] 

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Phoebe A. Rice]

Excellent point.  I've heard apocryphal stories of someone obtaining beautiful 
salt crystals (magnesium ammonium phosphate) by trying to crystallize an ATPase 
with ADP and Mg++ using (NH4)2SO4 as a precipitant.  Wait long enough, and the 
ADP becomes ATP plus AMP, the ATPase takes the 3rd phosphate off, and then the 
salt crystals grow.  

Yours sounds like a much less depressing "accident"!


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil Evans 
[p...@mrc-lmb.cam.ac.uk]
Sent: Thursday, January 19, 2017 4:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Remember that 2xADP can disproportionate into ATP + AMP

> On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan 
> <saravanan.panneersel...@desy.de> wrote:
>
> Dear All,
> Sorry for the little bit off topic. Is there a possibility for covalent
> bond formation between beta phosphate of ADP and acetate molecule both
> are coordinated by divalent metal ions? I am working on a Kinase
> structure  which was crystallized with ADP and in presence of 1M sodium
> acetate. We observed additional density around ADP that fits perfectly
> like a gamma phosphate , mimicking like ATP bound state, surrounded and
> coordinated by two metal ions(resolution is 1.4A). There is a change in
> space group (from I212121 to P212121 ) and further important
> conformation changes are observed around ATP binding pocket and distant
> region. This is the only xtal we obtained in this space group, and all
> other xtals(measured 10 xtals)  from the same plate belong to I212121.
>
>
>
> Thanks your help and time!
>
> Saravanan
> - Original Message -
> From: "CCP4BB automatic digest system" <lists...@jiscmail.ac.uk>
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Sunday, 15 January, 2017 01:01:37
> Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
>
> There are 2 messages totaling 45 lines in this issue.
>
> Topics of the day:
>
>   1. Phenix (2)
>
> --
>
> Date:Sat, 14 Jan 2017 20:58:09 +
> From:D Bonsor <dbon...@ihv.umaryland.edu>
> Subject: Phenix
>
> Is the phenix website down? Anyone know when it will be back up?
>
> --
>
> Date:Sat, 14 Jan 2017 14:45:06 -0800
> From:Pavel Afonine <pafon...@gmail.com>
> Subject: Re: Phenix
>
> See notice on Phenix mailing list that answers your question.
>
> On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor <dbon...@ihv.umaryland.edu>
> wrote:
>
>> Is the phenix website down? Anyone know when it will be back up?
>>
>
> --
>
> End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
> 

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Phil Evans]

Remember that 2xADP can disproportionate into ATP + AMP

> On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan 
>  wrote:
> 
> Dear All,
> Sorry for the little bit off topic. Is there a possibility for covalent 
> bond formation between beta phosphate of ADP and acetate molecule both 
> are coordinated by divalent metal ions? I am working on a Kinase 
> structure  which was crystallized with ADP and in presence of 1M sodium 
> acetate. We observed additional density around ADP that fits perfectly 
> like a gamma phosphate , mimicking like ATP bound state, surrounded and 
> coordinated by two metal ions(resolution is 1.4A). There is a change in 
> space group (from I212121 to P212121 ) and further important 
> conformation changes are observed around ATP binding pocket and distant 
> region. This is the only xtal we obtained in this space group, and all 
> other xtals(measured 10 xtals)  from the same plate belong to I212121.
> 
> 
> 
> Thanks your help and time!
> 
> Saravanan
> - Original Message -
> From: "CCP4BB automatic digest system" 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Sunday, 15 January, 2017 01:01:37
> Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
> 
> There are 2 messages totaling 45 lines in this issue.
> 
> Topics of the day:
> 
>   1. Phenix (2)
> 
> --
> 
> Date:Sat, 14 Jan 2017 20:58:09 +
> From:D Bonsor 
> Subject: Phenix
> 
> Is the phenix website down? Anyone know when it will be back up?
> 
> --
> 
> Date:Sat, 14 Jan 2017 14:45:06 -0800
> From:Pavel Afonine 
> Subject: Re: Phenix
> 
> See notice on Phenix mailing list that answers your question.
> 
> On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor 
> wrote:
> 
>> Is the phenix website down? Anyone know when it will be back up?
>> 
> 
> --
> 
> End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)
> 

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Phil Jeffrey]

On 1/19/17 3:54 PM, Panneerselvam, Saravanan wrote:

We observed additional density around ADP that fits perfectly
like a gamma phosphate


Hello Saravanan

At 1.4 Angstrom resolution wouldn't that suggest that you've somehow got 
ATP in there ?  I don't think I understand the other option - were you 
proposing a ADP-O-C(O)2 arrangement to explain the density ?  Surely 
that has a rather different shape, considerably different scattering 
power at the center of the terminal group (C vs P) and probably 
different X-O bond lengths.  All of these should show in the density 
maps at 1.4 Å, although the bond length issue could be quite subtle.


Phil Jeffrey
Princeton




mimicking like ATP bound state, surrounded and
coordinated by two metal ions(resolution is 1.4A). There is a change in
space group (from I212121 to P212121 ) and further important
conformation changes are observed around ATP binding pocket and distant
region. This is the only xtal we obtained in this space group, and all
other xtals(measured 10 xtals)  from the same plate belong to I212121.



Thanks your help and time!

Saravanan

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

[Panneerselvam, Saravanan]

Dear All,
Sorry for the little bit off topic. Is there a possibility for covalent 
bond formation between beta phosphate of ADP and acetate molecule both 
are coordinated by divalent metal ions? I am working on a Kinase 
structure  which was crystallized with ADP and in presence of 1M sodium 
acetate. We observed additional density around ADP that fits perfectly 
like a gamma phosphate , mimicking like ATP bound state, surrounded and 
coordinated by two metal ions(resolution is 1.4A). There is a change in 
space group (from I212121 to P212121 ) and further important 
conformation changes are observed around ATP binding pocket and distant 
region. This is the only xtal we obtained in this space group, and all 
other xtals(measured 10 xtals)  from the same plate belong to I212121.

 

Thanks your help and time!

Saravanan
- Original Message -
From: "CCP4BB automatic digest system" 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Sunday, 15 January, 2017 01:01:37
Subject: CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

There are 2 messages totaling 45 lines in this issue.

Topics of the day:

   1. Phenix (2)

--

Date:Sat, 14 Jan 2017 20:58:09 +
From:D Bonsor 
Subject: Phenix

Is the phenix website down? Anyone know when it will be back up?

--

Date:Sat, 14 Jan 2017 14:45:06 -0800
From:Pavel Afonine 
Subject: Re: Phenix

See notice on Phenix mailing list that answers your question.

On Sat, Jan 14, 2017 at 12:58 PM, D Bonsor 
wrote:

> Is the phenix website down? Anyone know when it will be back up?
>

--

End of CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Re: [ccp4bb] CCP4BB Digest - 10 Jan 2017 to 11 Jan 2017 (#2017-12)

[Whitley, Matthew J]

Hi Claire,

Isn’t the simplest answer just that the EDS server is calculating the 
completeness for a different amount of data (high res limit of 1.92 Å), whereas 
in your Depositor data it was only calculated to a high res limit of 2.1 Å?  
This would probably be the result of you measuring reflections out to 1.92 Å 
during data collection but then manually specifying a 2.1 Å high resolution 
cutoff during refinement.  The refinement program will calculate statistics 
based on your input limit of 2.1 Å, but if the MTZ file actually contains some 
measured data out to 1.92 Å, then the EDS would calculate a different, lower 
completeness if its default setting is simply to use all data present in the 
reflections file.  

Does that explain things, or do you actually have something else in mind as to 
the cause of the discrepancy?

Matthew

---
Matthew J. Whitley, Ph.D.
Research Associate
Angela Gronenborn Lab
Department of Structural Biology
University of Pittsburgh School of Medicine


> Date:Wed, 11 Jan 2017 17:31:38 -0500
> From:Claire Smith 
> Subject: PDB validation of structure factors
> 
> Hello,
> 
> I am trying to run the PDB validation report for a structure that I have
> refined in Phenix (data was analyzed with Xtriage). However, the run
> reports a discrepancy on the completeness of data, as follows:
> 
> % Data completeness  97.4 (29.08-2.10)   Depositor
> 
> (in resolution range)87.5 (29.08-1.92)EDS
> 
> 
> Why this discrepancy?
> 
> 
> Thanks so much,
> 
> Claire

Re: [ccp4bb] [ccp4bb] Remittance advice - Invitation to edit

[Anindito Sen]

my point exactly.

Andy


> On Dec 12, 2016, at 2:49 AM, Laura Spagnolo  
> wrote:
> 
> Isn't this mailing list moderated?
> Laura 
> 
> Sent from my iPhone
> 
> On 11 Dec 2016, at 17:48, Bonsor, Daniel  > wrote:
> 
>> The Nigerian Prince wants your money.
>> 
>> Get Outlook for Android 
>> From: CCP4 bulletin board > > on behalf of Anindito Sen 
>> >
>> Sent: Sunday, December 11, 2016 12:45:16 PM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit
>>  
>> Guys 
>> 
>> are you all receiving the same??? What on earth is this ?
>> 
>> Andy
>> 
>> 
>> 
>>> Begin forwarded message:
>>> 
>>> From: Hai-fu Fan >
>>> Subject: [ccp4bb] Remittance advice - Invitation to edit
>>> Date: December 12, 2016 at 2:31:56 AM GMT+9
>>> To: CCP4BB@JISCMAIL.AC.UK 
>>> Reply-To: Hai-fu Fan >
>>> 
>>> Please find attached for your review.
>>> Regards.
>>> 
>>> Hai-fu Fan
>> 
>> 

Re: [ccp4bb] CCP4BB Digest - 26 Nov 2016 to 27 Nov 2016 - Special issue (#2016-322)

[Laurence Pearl]

Picture of electron density didn’t come through, but three planar fused rings 
sounds like a flavin - is your protein involved in redox reactions and is it 
coloured when concentrated ? The only four ring molecules that spring to mind 
are steroids, but these wouldn’t be all that flat and you would get a sense of 
the pucker of the rings at that resolution.


On 27 Nov 2016, at 10:34, CCP4BB automatic digest system 
> wrote:

There are 2 messages totaling 65823 lines in this issue.

Topics in this special issue:

 1. Problems finding the correct Cif file of a crystal structure
 2. Density for an unknown ligand

--

Date:Sun, 27 Nov 2016 10:09:48 +
From:Harry Powell >
Subject: Re: Problems finding the correct Cif file of a crystal structure

Hi

Cambridge Structural Database (CSD) should have only those small molecule 
structures that have at least one organic carbon - so it may have copper 
acetate (but which? There may be several...). For strictly inorganic structures 
you would need the Inorganic Crystal Structural Database (ICSD).

Harry
--
Dr Harry Powell
Chairman of International Union of Crystallography Commission on 
Crystallographic Computing
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

On 26 Nov 2016, at 22:23, Eleanor Dodson 
> wrote:

There is a data bae - cambridge Structural Data Base with most crystal 
structures coordinates and measure data in it. if your university subscribes 
you should be able to acess it.
Eleanor dodson

On 26 November 2016 at 21:00, Bianca Valdes 
> wrote:
Hello!

I'm currently a PhD student. I'm taking a crystallography class and for our 
final project the professor wants us to compare the theoretical cif file of 
Copper Acetate with the experimental one we are generating. I found a cif file 
but is very incomplete,  do you guys now where I can find the complete and 
correct Cif file for Copper Acetate?


Thanks a lot!

Bianca


--

Date:Sun, 27 Nov 2016 18:33:34 +0800
From:Wei Liu >
Subject: Density for an unknown ligand

Dear all,

We have recently crystallized a recombinant protein produce from E. coli, and 
determined the structure at 1.9 Å. The asymmetric unit contains two protein 
monomers. Beyond our expectation, strong Fo - Fc density is present at a cleft 
of one subunit, but not in the other. Density maps are given in the snapshots 
attached to this email. We tried to model Tris or Bis-tris propane that were 
used as the purification and crystallization buffers, but apparently either of 
them poorly fitted in this density.  The molecule that can be modeled here 
seems more likely to be a ligand comprising 3 or 4 rings with good planarity, 
however we did not add any additives in our crystallization trials. So we think 
it should be something from E. coli, which has high affinity to our protein. I 
wonder if anybody can figure out which molecule well fits to the electron 
density.

Best wishes
Wei Liu




--

End of CCP4BB Digest - 26 Nov 2016 to 27 Nov 2016 - Special issue (#2016-322)
*


Laurence H. Pearl PhD FRS FMedSci

Professor of Structural Biology and Head of School of Life Sciences
University of Sussex, Brighton, BN1 9RH, UK

Phone +44-(0)1273 876 544: PA +44-(0)1273 872 699

"Live Modestly and do Serious Things .. "
- Dorothy Crowfoot Hodgkin

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

[Tristan Croll]

Sorry - didn't realise that was going out to the whole list, and just 
made a liar out of myself. Will bow out now.


On 2016-11-10 10:20, Tristan Croll wrote:

Hi Elton,

I certainly didn't say I agreed with their choice or thought it was a
good one. But as someone who grew up in a low-income, low-employment
environment myself this has the ring of truth to it. I totally agree
with you (and worry just as much) regarding the proliferation of
anti-expert sentiment - but I don't think it's necessarily the biggest
cause of what just happened in this case. It seems to me that a great
many people didn't vote for Trump because of who he was, but *in
spite* of who he was - given the choice between two people who they
perceived as corrupt, malevolent billionaires, they went for the one
who wasn't part of the political machine they see as irrevocably
broken, and at least said some things to indicate that he noticed
them. Essentially a protest vote, just on a country-wide scale. I just
hope the consequences won't be as severe as we all fear.

My personal answer to your final question comes in two parts:

(1) As I understand it, there's at least some indication that it isn't
as bad as it seems (or, more precisely, it's always been at least this
bad, but we just couldn't see it as clearly before). History is
littered with extreme examples of anti-science gaining control at the
highest levels of government (Lysenkoism, witch hunts, creationism,
etc.). At least these days it seems science is mostly on the front
foot (anti-science movements and politicians seem to be mostly
fighting a slowly losing battle against concepts introduced by
scientists, rather than scientists mostly fighting back against
unscientific dogma).

(2) A big part of the solution has to be in communication. Our ability
to communicate our work (and its importance) directly to the public
has never been greater. That "directly" bit is important, because
science journalists and even university PR departments have
historically had a habit of both mangling the science and overblowing
its impact between the scientist and the newsprint. Providing clear,
accessible and, above all, friendly explanations of key work online
can count for a heck of a lot.

Yes, we're certainly facing big problems - but I'm not yet ready to 
despair.


Best regards,

Tristan





On 2016-11-10 09:47, Elton Zeqiraj wrote:

Hi Tristan,

I’m afraid I don’t get the logic in the article you sent. In this
case the farmers who are crying for the attention of the people in
shiny palaces have voted for one who lives in golden mansions.

For me the really worrying thing here is how can so many people be
misled by a false prophet who lies and misbehaves so much. It is a
systemic problem in our society. We never before had so much access to
information, and yet it is so easy to mislead people.

People understood what Trump was and they basically said: “I don’t
care”! We are living in a world where people don’t care about
facts, they just say “I know it to be true”. As scientists whose
job and mission in life is to further and pass knowledge, it is very
serious that we are in this post-truth era. It affects us all when we
talk about climate change, evidence based treatments in our hospitals,
GM debate, etc.

Instead of making this about Trump, I would like to pose a different
question: How are we going to deal with the anti-expert movement that
is now so prominent in our society?

Cheers,
Elton


On Nov 10, 2016, at 8:15 AM, Tristan Croll  wrote:

In the interests of promoting understanding... the link below is to
an article on what is ostensibly a comedy website and contains a bit
of coarse language, but nevertheless is quite possibly the most
insightful exposition of the situation I've come across. The
two-sentence synopsis: don't think of this as the forces of hate,
fear and ignorance winning. Think of it as a cry for attention from
a large number of people who are seriously struggling and (mostly
correctly) see their problems as being ignored by the system.
Writing them off as ignorant and hateful isn't the answer.

In agreement with various others, this is my first and last post
referencing politics or religion on this forum.



http://www.cracked.com/blog/6-reasons-trumps-rise-that-no-one-talks-about/

[1]

On 2016-11-10 08:00, Marjolein Thunnissen wrote:
Dear Bill,
I fully agree with you, awareness has to be spread and one should
not
ignore politics completely, especially when there are so strong
anti-intellectual (anti-science) statements out there.
best regards
Marjolein
On 10 Nov 2016, at 04:17, William G. Scott  wrote:
Dear Edward et al:
I agree we shouldn’t engage in partisan arguments on the CCP4bb.
However, I think it is a mistake, and perhaps a missed opportunity,
to ignore politics completely.
For example, Newt Gingrich is currently in the running for Sec HHS.
He has previously written editorials in the NYT and Wall Street
Journal advocating 

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

[Tristan Croll]

Hi Elton,

I certainly didn't say I agreed with their choice or thought it was a 
good one. But as someone who grew up in a low-income, low-employment 
environment myself this has the ring of truth to it. I totally agree 
with you (and worry just as much) regarding the proliferation of 
anti-expert sentiment - but I don't think it's necessarily the biggest 
cause of what just happened in this case. It seems to me that a great 
many people didn't vote for Trump because of who he was, but *in spite* 
of who he was - given the choice between two people who they perceived 
as corrupt, malevolent billionaires, they went for the one who wasn't 
part of the political machine they see as irrevocably broken, and at 
least said some things to indicate that he noticed them. Essentially a 
protest vote, just on a country-wide scale. I just hope the consequences 
won't be as severe as we all fear.


My personal answer to your final question comes in two parts:

(1) As I understand it, there's at least some indication that it isn't 
as bad as it seems (or, more precisely, it's always been at least this 
bad, but we just couldn't see it as clearly before). History is littered 
with extreme examples of anti-science gaining control at the highest 
levels of government (Lysenkoism, witch hunts, creationism, etc.). At 
least these days it seems science is mostly on the front foot 
(anti-science movements and politicians seem to be mostly fighting a 
slowly losing battle against concepts introduced by scientists, rather 
than scientists mostly fighting back against unscientific dogma).


(2) A big part of the solution has to be in communication. Our ability 
to communicate our work (and its importance) directly to the public has 
never been greater. That "directly" bit is important, because science 
journalists and even university PR departments have historically had a 
habit of both mangling the science and overblowing its impact between 
the scientist and the newsprint. Providing clear, accessible and, above 
all, friendly explanations of key work online can count for a heck of a 
lot.


Yes, we're certainly facing big problems - but I'm not yet ready to 
despair.


Best regards,

Tristan





On 2016-11-10 09:47, Elton Zeqiraj wrote:

Hi Tristan,

I’m afraid I don’t get the logic in the article you sent. In this
case the farmers who are crying for the attention of the people in
shiny palaces have voted for one who lives in golden mansions.

For me the really worrying thing here is how can so many people be
misled by a false prophet who lies and misbehaves so much. It is a
systemic problem in our society. We never before had so much access to
information, and yet it is so easy to mislead people.

People understood what Trump was and they basically said: “I don’t
care”! We are living in a world where people don’t care about
facts, they just say “I know it to be true”. As scientists whose
job and mission in life is to further and pass knowledge, it is very
serious that we are in this post-truth era. It affects us all when we
talk about climate change, evidence based treatments in our hospitals,
GM debate, etc.

Instead of making this about Trump, I would like to pose a different
question: How are we going to deal with the anti-expert movement that
is now so prominent in our society?

Cheers,
Elton


On Nov 10, 2016, at 8:15 AM, Tristan Croll  wrote:

In the interests of promoting understanding... the link below is to
an article on what is ostensibly a comedy website and contains a bit
of coarse language, but nevertheless is quite possibly the most
insightful exposition of the situation I've come across. The
two-sentence synopsis: don't think of this as the forces of hate,
fear and ignorance winning. Think of it as a cry for attention from
a large number of people who are seriously struggling and (mostly
correctly) see their problems as being ignored by the system.
Writing them off as ignorant and hateful isn't the answer.

In agreement with various others, this is my first and last post
referencing politics or religion on this forum.



http://www.cracked.com/blog/6-reasons-trumps-rise-that-no-one-talks-about/

[1]

On 2016-11-10 08:00, Marjolein Thunnissen wrote:
Dear Bill,
I fully agree with you, awareness has to be spread and one should
not
ignore politics completely, especially when there are so strong
anti-intellectual (anti-science) statements out there.
best regards
Marjolein
On 10 Nov 2016, at 04:17, William G. Scott  wrote:
Dear Edward et al:
I agree we shouldn’t engage in partisan arguments on the CCP4bb.
However, I think it is a mistake, and perhaps a missed opportunity,
to ignore politics completely.
For example, Newt Gingrich is currently in the running for Sec HHS.
He has previously written editorials in the NYT and Wall Street
Journal advocating doubling the budget of the NIH.
I think it is incumbent upon us to make our voices heard if such an
opportunity arises, regardless 

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

[Elton Zeqiraj]

Hi Tristan,

I’m afraid I don’t get the logic in the article you sent. In this case the 
farmers who are crying for the attention of the people in shiny palaces have 
voted for one who lives in golden mansions. 

For me the really worrying thing here is how can so many people be misled by a 
false prophet who lies and misbehaves so much. It is a systemic problem in our 
society. We never before had so much access to information, and yet it is so 
easy to mislead people. 

People understood what Trump was and they basically said: “I don’t care”! We 
are living in a world where people don’t care about facts, they just say “I 
know it to be true”. As scientists whose job and mission in life is to further 
and pass knowledge, it is very serious that we are in this post-truth era. It 
affects us all when we talk about climate change, evidence based treatments in 
our hospitals, GM debate, etc.

Instead of making this about Trump, I would like to pose a different question: 
How are we going to deal with the anti-expert movement that is now so prominent 
in our society? 

Cheers,
Elton 



> On Nov 10, 2016, at 8:15 AM, Tristan Croll  wrote:
> 
> In the interests of promoting understanding... the link below is to an 
> article on what is ostensibly a comedy website and contains a bit of coarse 
> language, but nevertheless is quite possibly the most insightful exposition 
> of the situation I've come across. The two-sentence synopsis: don't think of 
> this as the forces of hate, fear and ignorance winning. Think of it as a cry 
> for attention from a large number of people who are seriously struggling and 
> (mostly correctly) see their problems as being ignored by the system. Writing 
> them off as ignorant and hateful isn't the answer.
> 
> In agreement with various others, this is my first and last post referencing 
> politics or religion on this forum.
> 
> http://www.cracked.com/blog/6-reasons-trumps-rise-that-no-one-talks-about/ 
> 
> 
> On 2016-11-10 08:00, Marjolein Thunnissen wrote:
>> Dear Bill,
>> I fully agree with you, awareness has to be spread and one should not
>> ignore politics completely, especially when there are so strong
>> anti-intellectual (anti-science) statements out there.
>> best regards
>> Marjolein
>>> On 10 Nov 2016, at 04:17, William G. Scott  wrote:
>>> Dear Edward et al:
>>> I agree we shouldn’t engage in partisan arguments on the CCP4bb.
>>> However, I think it is a mistake, and perhaps a missed opportunity,
>>> to ignore politics completely.
>>> For example, Newt Gingrich is currently in the running for Sec HHS.
>>> He has previously written editorials in the NYT and Wall Street
>>> Journal advocating doubling the budget of the NIH.
>>> I think it is incumbent upon us to make our voices heard if such an
>>> opportunity arises, regardless of what one may happen to think about
>>> the individual’s political orientation, as it could potentially be
>>> of enormous benefit to the scientific community.
>>> Yours faithfully,
>>> William G. Scott
>>> Director, Program in Biochemistry and Molecular Biology
>>> Professor, Department of Chemistry and Biochemistry
>>> and The Center for the Molecular Biology of RNA
>>> University of California at Santa Cruz
>>> Santa Cruz, California 95064
>>> USA
>>> http://scottlab.ucsc.edu  [1]
 On Nov 9, 2016, at 9:02 AM, Edward Snell >
 wrote:
 As a Brexit and Trumpet affected person having a foot in both
 countries ,this topic is too far off the normal discussion on CCP4
 and probably better taken up privately. CCP4 is not a political
 discussion site. With CCP4 the signal is unusually high and the
 noise low when compared to any discussion board. I for one would
 like to keep it there. Political views aside, we’re all trying
 to achieve the same scientific goals. Let’s remember that and
 keep that the focus.
 Edward Snell Ph.D.
 President and CEO Hauptman-Woodward Medical Research Institute
 Assistant Prof. Department of Structural Biology, University at
 Buffalo
 700 Ellicott Street, Buffalo, NY 14203-1102
 Phone: (716) 898 8631 Fax: (716) 898 8660
 Skype: eddie.snell Email: esn...@hwi.buffalo.edu 
 
 
 Heisenberg was probably here!
>> DR. MARJOLEIN THUNNISSEN
>> Head User Office
>> MAX IV Laboratory
>> Lund University
>> P.O. Box 118, SE-221 00 Lund, Sweden
>> Visiting address: Fotongatan 2, 225 94 Lund
>> Telephone: +46 46 2224668
>> Mobile: +46 766 32 04 17
>> www.maxliv.lu.se  [2]
>> Links:
>> --
>> [1] http://scottlab.ucsc.edu 
>> [2] http://www.maxlab.lu.se/ 

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

[Phil Evans]

From letters in yesterday’s Guardian:-

today is 9/11

Make America grate again



> On 10 Nov 2016, at 08:00, Marjolein Thunnissen 
>  wrote:
> 
> Dear Bill,
> 
> I fully agree with you, awareness has to be spread and one should not ignore 
> politics completely, especially when there are so strong anti-intellectual 
> (anti-science) statements out there.
> 
> best regards
> 
> Marjolein
> 
>> On 10 Nov 2016, at 04:17, William G. Scott  wrote:
>> 
>> Dear Edward et al:
>> 
>> I agree we shouldn’t engage in partisan arguments on the CCP4bb.  However, I 
>> think it is a mistake, and perhaps a missed opportunity, to ignore politics 
>> completely.
>> 
>> For example, Newt Gingrich is currently in the running for Sec HHS.  He has 
>> previously written editorials in the NYT and Wall Street Journal advocating 
>> doubling the budget of the NIH.  
>> 
>> I think it is incumbent upon us to make our voices heard if such an 
>> opportunity arises, regardless of what one may happen to think about the 
>> individual’s political orientation, as it could potentially be of enormous 
>> benefit to the scientific community.
>> 
>> Yours faithfully,
>> 
>> William G. Scott
>> Director, Program in Biochemistry and Molecular Biology
>> Professor, Department of Chemistry and Biochemistry
>> and The Center for the Molecular Biology of RNA
>> University of California at Santa Cruz
>> Santa Cruz, California 95064
>> USA
>> 
>> http://scottlab.ucsc.edu
>> 
>>> On Nov 9, 2016, at 9:02 AM, Edward Snell  wrote:
>>> 
>>> As a Brexit and Trumpet affected person having a foot in both countries 
>>> ,this topic is too far off the normal discussion on CCP4 and probably 
>>> better taken up privately.  CCP4 is not a political discussion site. With 
>>> CCP4 the signal is unusually high and the noise low when compared to any 
>>> discussion board. I for one would like to keep it there. Political views 
>>> aside, we’re all trying to achieve the same scientific goals. Let’s 
>>> remember that and keep that the focus.
>>> 
>>> Edward Snell Ph.D.
>>> President and CEO Hauptman-Woodward Medical Research Institute
>>> Assistant Prof. Department of Structural Biology, University at Buffalo
>>> 700 Ellicott Street, Buffalo, NY 14203-1102
>>> Phone: (716) 898 8631 Fax: (716) 898 8660
>>> Skype:  eddie.snell Email: esn...@hwi.buffalo.edu 
>>> 
>>> Heisenberg was probably here!
> 
> 
> 
> 
> 
> 
> 
> 
> Dr. Marjolein Thunnissen
> Head User Office
> 
> MAX IV Laboratory
> Lund University
> P.O. Box 118, SE-221 00 Lund, Sweden
> Visiting address: Fotongatan 2, 225 94 Lund
> Telephone:+46 46 2224668
> Mobile:  +46 766 32 04 17
> www.maxliv.lu.se
> 
> 

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

[Marjolein Thunnissen]

Dear Bill,

I fully agree with you, awareness has to be spread and one should not ignore 
politics completely, especially when there are so strong anti-intellectual 
(anti-science) statements out there.

best regards

Marjolein

On 10 Nov 2016, at 04:17, William G. Scott 
> wrote:

Dear Edward et al:

I agree we shouldn’t engage in partisan arguments on the CCP4bb.  However, I 
think it is a mistake, and perhaps a missed opportunity, to ignore politics 
completely.

For example, Newt Gingrich is currently in the running for Sec HHS.  He has 
previously written editorials in the NYT and Wall Street Journal advocating 
doubling the budget of the NIH.

I think it is incumbent upon us to make our voices heard if such an opportunity 
arises, regardless of what one may happen to think about the individual’s 
political orientation, as it could potentially be of enormous benefit to the 
scientific community.

Yours faithfully,

William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA

http://scottlab.ucsc.edu

On Nov 9, 2016, at 9:02 AM, Edward Snell  wrote:

As a Brexit and Trumpet affected person having a foot in both countries ,this 
topic is too far off the normal discussion on CCP4 and probably better taken up 
privately.  CCP4 is not a political discussion site. With CCP4 the signal is 
unusually high and the noise low when compared to any discussion board. I for 
one would like to keep it there. Political views aside, we’re all trying to 
achieve the same scientific goals. Let’s remember that and keep that the focus.

Edward Snell Ph.D.
President and CEO Hauptman-Woodward Medical Research Institute
Assistant Prof. Department of Structural Biology, University at Buffalo
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu

Heisenberg was probably here!

[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]






Dr. Marjolein Thunnissen
Head User Office

MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Telephone:+46 46 2224668
Mobile:  +46 766 32 04 17
www.maxliv.lu.se

Re: [ccp4bb] [ccp4bb] on NCS restraint

[Reza Khayat]

Hi,

The purpose of NCS is to reduce the degrees of freedom in order to avoid over 
refinement -not only to expedite refinement. Strict or restrained NCS should be 
applied at lower resolutions (2.7Å) or data completeness. Forgo NCS If you 
have a complete and better than 2.5Å dataset. Also, you can define the regions 
where NCS is applied and thus avoid loops/regions where the NCS is violated.

Best wishes,
Reza

Reza Khayat, PhD
Assistant Professor
City College of New York
160 Convent Ave, MR-1135
New York, NY 10031
(212) 650-6070
rkha...@ccny.cuny.edumailto:rkha...@ccny.cuny.edu


On Apr 20, 2015, at 4:01 AM, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:

Dear Smith,

There used to be something called “strict NCS“ which meant that instead of many 
identical subunits, only one “average” subunit was refined, which would speed 
up the refinement significantly, at the expense of requiring that all subunits 
are exactly identical.

I do not think that this option is used anymore and most refinement programs 
would require NCS related subunits to be similar, but not identical to each 
other. As Robbie Joosten pointed at, this can help a lot, especially when you 
do not have high resolution data. So for data with better than 2.0 Å 
resolution, including NCS restraints would probably not make a big difference, 
but otherwise I would switch them on.

Best,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Smith Liu
Gesendet: Freitag, 17. April 2015 06:02
An: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] on NCS restraint

Dear Jurgen,

My understanding is that NCS restraint can significantly enhance the speed of 
calculation, but considering the subunits even with the eactly same sequence 
may not be identical, to have NCS restraint may be not necessary or may be not 
good for the refinement, am I right?

Smith




At 2015-04-17 09:09:05, Jurgen Bosch 
jbos...@jhu.edumailto:jbos...@jhu.edu wrote:

yes.
Have two sets of NCS operators one that describe the four subunits and one 
describing the two subunits. If during the refinement of your structure you 
should find out that the subunits are not identical to each other you can relax 
the NCS weights.

Jürgen
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742tel:%2B1-410-614-4742
Lab:  +1-410-614-4894tel:%2B1-410-614-4894
Fax:  +1-410-955-2926tel:%2B1-410-955-2926
http://lupo.jhsph.eduhttp://lupo.jhsph.edu/

On Apr 16, 2015, at 9:02 PM, Smith Lee 
0459ef8548d5-dmarc-requ...@jiscmail.ac.ukmailto:0459ef8548d5-dmarc-requ...@jiscmail.ac.uk
 wrote:


Dear All,

If a protein contains 6 subunits, 4 subunits from the same sequence (subunit A, 
B, C, D all from the same sequence), each of the 2 other subunits from 2 
diffrent sequences (subunit E from the second sequence, subunit F from the 
third sequence), in this situation should I use NCS restraint or not?

If my protein contains 2 subunits, both of the 2 subunits composed of the 
eaxctly same sequence, however supposing the 2 subunits have a little diffrent 
conformation, in this situation should we use NCS retraint or not?

Smith

Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92)

[dusan turk]

Shane,

After you define which segments share proper or improper all NCS their 
parameters in MAIN environment, they will be calculated and stored in such 
macro files. 

$ cat mol_A_to_B.com 
! SAVING RMS FIT DATA: 
set matrix MAT_ROT number - 
  0.959598  -0.031620  -0.279592 - 
 -0.029443   0.976927  -0.211536 - 
  0.279830   0.211222   0.936526 
set vari XTRAN global real = 3.66 
set vari YTRAN global real =   105.12 
set vari ZTRAN global real =   -33.40 
return 

If you want to renormalize your matrices, you not only need to ensure that the 
length of your lines or columns is equal to 1, but also that they are 
orthogonal to each other, which is the easiest achieved by calculating the 
cross products of the matrix lines (a,b,c): (a * b = c ) through which you 
calculate first c and then either a or b.  I would not do it, because  the 
limited precision distorts the transformation and making in orthogonal will 
distort the accuracy of superimposition.

best,
dusan



 On Apr 3, 2015, at 1:00 AM, CCP4BB automatic digest system 
 lists...@jiscmail.ac.uk wrote:
 
 
 Date:Wed, 1 Apr 2015 20:47:25 -0400
 From:Shane Caldwell shane.caldwel...@gmail.com
 Subject: Re: Sortwater NCS Matrix input
 
 Alright, thanks! It's a good thing, then, I spent the afternoon brushing up
 on matrices.
 
 I guess the next, probably more general question for the bb is: which
 utilities export an NCS transformation matrix with more precision?
 *superpose* and *gesamt* only export three decimals, though I'm sure they
 use greater precision under the hood. I'm not opposed to exporting from
 coot or pymol either, I just haven't figured out how to do this yet - what
 would be the simplest way to calculate and export an NCS transformation
 matrix?
 
 Shane
 

Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
Professor of Structural Biology at IPS Jozef Stefan
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem. Mol. Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com

Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92)

[Robert Esnouf]

Dear Shane,

Many, many years ago in a different world (BobScript), I got around these 
issues using Gram-Schmidt Orthogonalization:

http://en.wikipedia.org/wiki/Gram%E2%80%93Schmidt_process

I adapted it in Fortran, but you're welcome to it... but you can probably find 
it in a more modern library now.

Regards,
Robert

--

Dr. Robert Esnouf,

University Research Lecturer,
Head of Research Computing Core,
NDM Research Computing Strategy Officer

Room 10/028, Wellcome Trust Centre for Human Genetics,
Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK

Email: rob...@strubi.ox.ac.uk / rob...@well.ox.ac.uk
Tel:   (+44) - 1865 - 287783


 Original message 
Date: Fri, 3 Apr 2015 08:44:59 +0200
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of dusan turk 
dusan.t...@ijs.si)
Subject: Re: [ccp4bb] CCP4BB Digest - 1 Apr 2015 to 2 Apr 2015 (#2015-92)  
To: CCP4BB@JISCMAIL.AC.UK

Shane,

After you define which segments share proper or improper all NCS their 
parameters in MAIN environment, they will be calculated and stored in such 
macro files. 

$ cat mol_A_to_B.com 
! SAVING RMS FIT DATA: 
set matrix MAT_ROT number - 
  0.959598  -0.031620  -0.279592 - 
 -0.029443   0.976927  -0.211536 - 
  0.279830   0.211222   0.936526 
set vari XTRAN global real = 3.66 
set vari YTRAN global real =   105.12 
set vari ZTRAN global real =   -33.40 
return 

If you want to renormalize your matrices, you not only need to ensure that the 
length of your lines or columns is equal to 1, but also that they are 
orthogonal to each other, which is the easiest achieved by calculating the 
cross products of the matrix lines (a,b,c): (a * b = c ) through which you 
calculate first c and then either a or b.  I would not do it, because  the 
limited precision distorts the transformation and making in orthogonal will 
distort the accuracy of superimposition.

best,
dusan



 On Apr 3, 2015, at 1:00 AM, CCP4BB automatic digest system 
 lists...@jiscmail.ac.uk wrote:
 
 
 Date:Wed, 1 Apr 2015 20:47:25 -0400
 From:Shane Caldwell shane.caldwel...@gmail.com
 Subject: Re: Sortwater NCS Matrix input
 
 Alright, thanks! It's a good thing, then, I spent the afternoon brushing up
 on matrices.
 
 I guess the next, probably more general question for the bb is: which
 utilities export an NCS transformation matrix with more precision?
 *superpose* and *gesamt* only export three decimals, though I'm sure they
 use greater precision under the hood. I'm not opposed to exporting from
 coot or pymol either, I just haven't figured out how to do this yet - what
 would be the simplest way to calculate and export an NCS transformation
 matrix?
 
 Shane
 

Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
Professor of Structural Biology at IPS Jozef Stefan
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem. Mol. Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com

Re: [ccp4bb] CCP4BB Digest - 25 Mar 2015 to 26 Mar 2015 (#2015-86)

[dusan turk]

Dear Herman,

I am not sure what you really want. Maybe this can help you.

You can get the following numbers out of MAIN 
1. comparing a pair of selections. It makes sense only if they are equivalent.

 rms b-val  select my_selection_1 end select my_selection_2 end

2. Show command does statistics for a given selection. The “bond keyword 
considers fluctuations between bonding atoms, whereas without it the selection 
is considered as one group. 

 show b-val bond select my_selection end

best regards,
dusan


 On Mar 27, 2015, at 1:00 AM, CCP4BB automatic digest system 
 lists...@jiscmail.ac.uk wrote:
 
 Date:Thu, 26 Mar 2015 11:32:43 +
 From:herman.schreu...@sanofi.com mailto:herman.schreu...@sanofi.com
 Subject: r.m.s.d. ΔB
 
 Dear Bulletin Board,
 
 A referee wants for the “Table 1” in the supplementary information the 
 following data:
 
 The r.m.s.d. ΔB (bonded atoms) (Å2)
 All protein atoms
 Main chain – Main chain
 Side chain – Side chain
 Main chain – Side chain
 
 r.m.s.d. ΔB (Non-bonded contacts) (Å2)
 All protein atoms
 
 Using google I found at that some of these numbers could be calculated with 
 Moleman, although I am not sure to what extend this program is still 
 maintained.
 Older versions of Refmac would calculate r.m.s.d. ΔB’s for main chain and 
 side chain bonds, which I guess would be the “Main chain – Main chain” and 
 “Side chain – Side chain” values requested. However, what would should I 
 think of the “Main chain – Side chain” values; differences between Calpha and 
 Cbeta atoms?
 
 What would be the use of these numbers? The standard CCP4 validation 
 programs, or any validation program I know, do not calculate these numbers, 
 so they do not seem to be extremely important. If somebody could point me to 
 a program which could calculate these number without too much effort, I would 
 be happy to do it.  Otherwise, I would still be willing to go the extra mile 
 if someone could convince me that it is useful to have these numbers.
 
 Thank you for your help!
 Herman
 

Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/ 
http://bio.ijs.si/sbl/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
Professor of Structural Biology at IPS Jozef Stefan
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem. Mol. Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com http://www.skype.com/

Re: [ccp4bb] CCP4BB Digest - 28 Feb 2015 to 1 Mar 2015 (#2015-61)

[Jim Pflugrath]

Instead of Br which has a weak signal at its K edge, why not use Iodide at
some wavelength (or energy) where it gives a stronger signal?  The longer
wavelength used will help with spot spatial resolution as well.

One may be fighting radiation damage, too.
One may be fighting a moving (vibrating?) crystal, too.

Sure, you already have some diffraction images, but a better experiment may
make one's life easier.

My advice would be to not use higher than a 200 mM (4% saturated) KI quick
soak, but you didn't tell us how Br ended up in your crystals.

Jim

Recently, I got some datasets with weak anomalous Br signal. I tried to
 merge them according to  Q. Liu et al Science 336, p1033 (2012). I am using
 the script multiscale@SSRL. The merged dataset has WEAKER anomalous
 signals.

 Liu et al used SCALA for scaling and merging while multiscale@SSRL using
 AIMLESS. Should this cause such a difference? The SCALA@SSRL has a
 limitation on the number of frames it can process. So I cannot directly
 check if this caused the difference.

 Any suggestions?

Re: [ccp4bb] CCP4BB Digest - 5 Feb 2015 to 6 Feb 2015 (#2015-40)

[dusan turk]

Fred,

as you know discontinuous lattice is not physically possible. Therefore first 
make sure  to exclude your and deposition errors like a wrong space group and 
cell constants. However, it may be that some molecules are disordered and 
therefore absent in the structure solution. If there are no described errors, 
it is possible that it is similar case to the structure we published last year: 
Renko et al., 
Partial rotational lattice order–disorder in stefin B crystals. 
Acta Crystallogr D Biol Crystallogr. 2014 Apr 1; 70(Pt 4): 1015–1025.
Published online 2014 Mar 19. doi:  10.1107/S139900471491
PMCID: PMC3975888

best regards,
dusan



 On Feb 7, 2015, at 1:00 AM, CCP4BB automatic digest system 
 lists...@jiscmail.ac.uk wrote:
 
 
 Date:Fri, 6 Feb 2015 11:58:45 +0100
 From:Kerff Fred fke...@ulg.ac.be
 Subject: Absence of contact between layers in a crystal
 
 Hello,
 
 Looking at structure 2HR0 (The structure of complement C3b provides insights 
 into complement activation and regulation. »,Abdul Ajees, A.,  Gunasekaran, 
 K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna Murthy, H.M.;  
 (2006) Nature 444: 221-225), I noticed the absence of contacts between layers 
 in the crystal. Is it something that has already been observed in other 
 crystals?
 
 Best regards,
 
 Fred
 -
 Frédéric Kerff
 Chercheur qualifié F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège

Dr. Dusan Turk, Prof.
Head of Structural Biology Group http://bio.ijs.si/sbl/ 
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
http://www.cipkebip.org/
Professor of Structural Biology at IPS Jozef Stefan
e-mail: dusan.t...@ijs.si
phone: +386 1 477 3857   Dept. of Biochem. Mol. Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com

Re: [ccp4bb] CCP4BB Digest - 20 Dec 2014 to 21 Dec 2014 (#2014-38)

[Martha Quesada]

Please remove me from your mailing list.


On 12/21/14, 7:00 PM, CCP4BB automatic digest system
lists...@jiscmail.ac.uk wrote:

 There are 2 messages totaling 244 lines in this issue.
 
 Topics of the day:
 
   1. Cross-validation when test set is miniscule
   2. non-specific disulfide bonds in crystal structures
 
 --
 
 Date:Sat, 20 Dec 2014 17:41:00 -0800
 From:Axel Brunger brun...@stanford.edu
 Subject: Re: Cross-validation when test set is miniscule
 
 Dear Derek,
 
 I suggest you try 10% for the test set.  You should still be able to judge the
 effect of 
 various restraints (or constraints) as long as you keep the same test set.  If
 you switch test sets, and re-refine, Rfree
 might change as much as 2% for a test set consisting of 200 reflections - see
 Fig. 6 in  ref. (A. T. Brunger, Free
 R value: Cross-validation in crystallography, Methods in Enzym. 277, 366-396,
 1997). However, using the
 same test set may allow you to judge the best restraints protocol or weights.
 
 Axel
 
 PS: The Methods in Enzym. review also briefly discusses complete
 cross-validation.
 
 PPS: For refinement at very low resolution, see also:
 
 A.T.Brunger, P.D.Adams, P.Fromme, R.Fromme, M.Levitt, G.F. Schroder. Improving
 the accuracy of 
 macromolecular structure refinement at 7 A resolution. Structure 20, 957-966
 (2012).
 
 
 On Dec 20, 2014, at 1:05 AM, CCP4BB automatic digest system
 lists...@jiscmail.ac.uk wrote:
 
 Date:Fri, 19 Dec 2014 11:18:37 +
 From:Derek Logan derek.lo...@biochemistry.lu.se
 Subject: Cross-validation when test set is miniscule
 
 Hi everyone,
 
 Right now we have one of those very difficult Rfree situations where it's
 impossible to generate a single meaningful Rfree set. Since we're in a bit of
 a hurry with this structure it would be good if someone could point me in the
 right direction. We have crystals with 1542 non-H atoms in the asymmetric
 unit that diffract to only 3.6 Å in P65, which gives us a whopping 2300
 reflections in total. 5% of this is only about 100 reflections. Luckily the
 protein is only a single point mutation of a wild type that has been solved
 to much better resolution, so we know what it should look like and I simply
 want to investigate the effect of different levels of conservatism in the
 refinement, e.g. NCS in xyz and B, group B-factors, reference model,
 Ramachandran restraints etc. However since the quality criterion for this is
 Rfree I'm not able to do this.
 
 I believe the correct approach is k-fold statistical cross-validation, but
 can someone remind me of the correct way to do this? I've done a bit of
 Googling without finding anything very helpful.
 
 Thanks
 Derek
 
 Derek Logan tel: +46 46 222 1443
 Associate Professor mob: +46 76 8585 707
 Dept. of Biochemistry and Structural Biology
 www.cmps.lu.sehttp://www.cmps.lu.se
 Centre for Molecular Protein Sciencewww.maxlab.lu.se/crystal
 Lund University, Box 124, 221 00 Lund, Sweden   www.saromics.com
 
 Axel T. Brunger
 Investigator,  Howard Hughes Medical Institute
 Professor and Chair, Dept. of Molecular and Cellular Physiology
 Stanford University
 
 Web:http://atbweb.stanford.edu
 Email:  brun...@stanford.edu
 Phone:  +1 650-736-1031
 
 --
 
 Date:Sun, 21 Dec 2014 10:14:00 +0100
 From:mesters mest...@biochem.uni-luebeck.de
 Subject: Re: non-specific disulfide bonds in crystal structures
 
 Hello Todd,
 
 if your protein is a cytosolic protein (reductive environment; for ER,
 Golgi, mitochondria things look different), the disulfide bond formation
 you observe is most probably the result of the oxidative environment
 (outside the cell) in combination with the crystal packing that that
 brings the two cysteins in close proximity.
 
 J.
 
 
 Am 20.12.14 um 18:52 schrieb Todd Jason Green:
 Hello All-
 
 I have recently determined a domain structure of a larger protein. The
 structure shows a clear disulfide bond between two monomers in the
 asymmetric unit. I'm trying to figure out if this is an artifact of
 the crystal packing or has biological relevance. The protein has been
 reported to function as a monomer. If I look at the pool of protein on
 a SDS-PAGE gel under non-reducing conditions, I see that a smaller
 percentage (~15-20%) of the protein runs as a dimer. In the structure,
 the association has 2-fold symmetry with about 29% of the monomeric
 surface area buried between the dimer. Can anyone point me in the
 direction of a paper describing a non-specific disulfide in a crystal,
 or perhaps a criteria for assessing specificity? I will do some
 functional studies, but I'm looking for some info on a lazy saturday.
 
 Thanks in advance. Best-
 Todd
 

Re: [ccp4bb] CCP4BB Digest - 13 Aug 2014 to 14 Aug 2014 (#2014-220)

[Jack Reynolds]

Unsubscribe


Sent via the Samsung GALAXY S®4, an ATT 4G LTE smartphone

div Original message /divdivFrom: CCP4BB automatic digest 
system lists...@jiscmail.ac.uk /divdivDate:08/14/2014  6:00 PM  
(GMT-06:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: CCP4BB 
Digest - 13 Aug 2014 to 14 Aug 2014 (#2014-220) /divdiv
/divThere are 17 messages totaling 1766 lines in this issue.

Topics of the day:

  1. Off topic: Cloning multi genes/multi cistronic in yeast
  2. software/web server to determine ligand volume
  3. Question about Pilatus2M with denzo and xdisp
  4. Difference between different b factors values (2)
  5. CC-half value
  6. AW: [ccp4bb] Difference between different b factors values
  7. Twinning in space group Pc
  8. Kinase postdoc positions available at SGC, Oxford University
  9. desiring untouched ligand (2)
10. CC-half value ?? (3)
11. monomer/dimer protein
12. dynapro DLS cuvettes (2)

--

Date:Wed, 13 Aug 2014 15:51:57 -0700
From:Karsten Thierbach thier...@caltech.edu
Subject: Re: Off topic: Cloning multi genes/multi cistronic in yeast

Hey,
in my old lab we developed a system to express two proteins from one 
plasmid using the before mentioned GAL1-10 Promoter. Giving the use of 
different plasmids with different selection markers, coexpression of 
multiple proteins is possible in yeast.  The system was used in a study 
published in Structure last year and you could contact my old lab to 
request plasmids. We used a TRP1 and a LEU2 plasmid and coexpressed 
three proteins in this study, but it is easily extendable to at least 4 
proteins.
You can find the paper here:
http://www.ncbi.nlm.nih.gov/pubmed/23954503
To receive plasmids from the study, please contact Ed Hurt, the 
corresponding author at the BZH in Heidelberg/Germany.
I stumbled across a similar system recently, which is also based on the 
GAL promoter, but don't find the reference now...
Good luck,
Karsten

Am 13.08.2014 15:31, schrieb Chris Putnam:
 On 8/13/14 2:29 PM, Theresa Hsu wrote:
 Dear all

 One of my human membrane proteins have been described to interact 
 with additional subunits for its activity. To obtain functional form 
 in yeast (Saccharomyces), I can think of two approach of either 
 cloning all the subunits under one promoter or reconstitute in vitro.

 For the first option, what is the length of base pairs between the 
 stop codon of one gene and the start of Kozak sequence for the next 
 one? Is there any preference for the order so that only one subunit 
 is His tagged?

 Second option will need multiple purification steps and some trials 
 with protein ratios. Is this better?



 Natively, Saccharomyces does not have operons. And I am unaware of 
 operon-like constructs (single promoter with multiple genes oriented 
 in the same direction) working in Saccharomyces.  (The GAL1-10 
 divergent promoter is probably the closest analog, but this involves 
 transcription of the GAL1 and GAL10 genes that are encoded on opposite 
 strands in opposite orientations.)

 For multiprotein complexes, one strategy for in vivo complex assembly 
 is to encode each protein (with its own promoter) on separate plasmid 
 (with distinct selectable markers) and transform them all into the 
 same strain. This avoids the problems of in vitro reconstitution of 
 the complex as well as the problem of subunits that cannot be stably 
 expressed alone.

 Chris.

-- 
Karsten Thierbach, Dr. rer. nat.

California Institute of Technology
Division of Chemistry  Chemical Engineering
Hoelz laboratory

1200 E. California Blvd., M/C 147-75
Pasadena, CA 91125, U.S.A.

--

Date:Wed, 13 Aug 2014 17:19:14 -0600
From:Javier Gonzalez bio...@gmail.com
Subject: Re: software/web server to determine ligand volume

You can calculate volumes and much more, here:

http://www.molinspiration.com/cgi-bin/properties

Javier


On Wed, Aug 13, 2014 at 12:06 AM, sreetama das somon_...@yahoo.co.in
wrote:

 Dear all,
 Is there any software or web server available to calculate the volume of a
 ligand if the ligand coordinates are provided?
 Google seems to come up only with options to calculate protein cavity
 volume.

 Thanks in advance,
 Sreetama Das,
 phd student,
 Physics, IISc




-- 
Javier M. Gonzalez, PhD.
Protein Crystallography Station
Bioscience Division
Bioenergy and Biome Sciences Group (B-11)
Los Alamos National Laboratory
TA-3, Building 4200, Room 202B
Mailstop T007
Los Alamos, NM 87545
Phone: +1 (505) 667-9376
LinkedIn http://www.linkedin.com/pub/javier-gonz%C3%A1lez/22/7b/83a Email
bio...@gmail.com

--

Date:Thu, 14 Aug 2014 09:25:15 +0300
From:Meytal Landau landau.mey...@gmail.com
Subject: Re: Question about Pilatus2M with denzo and xdisp

For all who are interested in this issue: HKL people solved the problem.
The command for xdisp and denzo is:ccd 2m-pilatuscbf
The def.site is also