Re: [ccp4bb] Insturct-ERIC msg from Joel - [ccp4bb] Instruct Funded Access Call - Early Career Research Call: Submit by 31 July!

[Joel Sussman]

On 12 Jul 2024, at 11:12, ccp4mail  wrote:

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Dear All,

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Re: [ccp4bb] Unknown density

[Rafael Marques]

Dear John

Ethanol would be my first guess,

Best wishes


__

Rafael Marques da Silva

PhD Student – Structural Biology

University of Leicester

Mestrando em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"


De: CCP4 bulletin board  em nome de John Smith 

Enviado: quinta-feira, 11 de julho de 2024 09:35
Para: CCP4BB@JISCMAIL.AC.UK 
Assunto: [ccp4bb] Unknown density

Dear all!
We have solved a structure at 2.2 A resolution. We see this interesting density 
near a Tyrosine. It is not fully aligned, like pi stacking. Otherwise, 
negatively charged or polar residues surround the smaller 'head'.

Does anybody have any idea?

Thanks for the help!

Best
John




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Re: [ccp4bb] message yesterday on the CCP4BB

[Tim Gruene]

On Wed, 10 Jul 2024 08:46:06 +
"Hough, Michael (DLSLtd,RAL,LSCI)"
<69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote:

> or the magic porridge pot...
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Harry
> Powell Sent: Wednesday, July 10, 2024 9:43 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] message yesterday on the CCP4BB
> 
> Hi
> 
> Pandora's box comes to mind...

It's called 'internet' 
Cheers,
Tim

-- 
--
Tim Gruene
Head of the Core Facility Crystal Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

https://ccsa.univie.ac.at

GPG Key ID = A46BEE1A



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pgpyiF2tmtVaq.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] message yesterday on the CCP4BB

[Hough, Michael (DLSLtd,RAL,LSCI)]

or the magic porridge pot...

-Original Message-
From: CCP4 bulletin board  On Behalf Of Harry Powell
Sent: Wednesday, July 10, 2024 9:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] message yesterday on the CCP4BB

Hi

Pandora's box comes to mind...

Harry

> On 10 Jul 2024, at 07:14, Grant Hansman 
> <db9e83c7f6ed-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi,
>
> I sent a message yesterday on the CCP4BB (below). I received so many 
> enquires. Can I edit or stop this message as I no longer need help. The 
> community was so helpful!
>
> Best,
> Grant
>
>
> Subject:
>
> 
> Looking for a student and/or help with finalizing new virus spike
> structures
>
> From:
>
> 
> Grant Hansman g.hans...@griffith.edu.au
>
> Reply-To:
>
> 
> Grant Hansman g.hans...@griffith.edu.au
>
> Date:
>
> 
> Tue, 9 Jul 2024 05:52:35 +0100
>
> Content-Type:
>
> 
> text/plain
>
> Parts/Attachments:
>
> 
> 
> text/plain (17 lines)
>
> 
> 
> Reply
>
> Help needed ASAP.
>
> I am just setting up my new laboratory in Australia (alone at the moment) and 
> already have at least 5 new X-ray structures that need checking and a bit 
> more refinement. High resolution and should not be too much work.
>
> Therefore, I am looking for a student with experience and/or any help with 
> finalizing the structures (will provide all details to those interested).
>
> Happy to add as a co-first author to any manuscripts, as all the wet
> lab, data collection, and refinements were done by myself ;)
>
> Cheers.
>
>
>
> Dr Grant Hansman | Senior Research Fellow
>
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for
> Glycomics (G25) Room 2.56 T +61 7 5552 9552 | E
> g.hans...@griffith.edu.au
>
> griffith.edu.au/institute-glycomics
> 
> Griffith University - CRICOS Provider Number 00233E PRIVILEGED -
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> To unsubscribe from the CCP4BB list, click the following link:
> https://www/.
> jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=
> 05%7C02%7Cmichael.hough%40DIAMOND.AC.UK%7C83eb7b53894949e60ea708dca0bc
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Re: [ccp4bb] message yesterday on the CCP4BB

[Harry Powell]

Hi

Pandora’s box comes to mind…

Harry

> On 10 Jul 2024, at 07:14, Grant Hansman 
>  wrote:
> 
> Hi,
>  
> I sent a message yesterday on the CCP4BB (below). I received so many 
> enquires. Can I edit or stop this message as I no longer need help. The 
> community was so helpful!
>  
> Best,
> Grant
>  
>  
> Subject:
> 
> 
> Looking for a student and/or help with finalizing new virus spike structures
> 
> From:
> 
> 
> Grant Hansman g.hans...@griffith.edu.au
> 
> Reply-To:
> 
> 
> Grant Hansman g.hans...@griffith.edu.au
> 
> Date:
> 
> 
> Tue, 9 Jul 2024 05:52:35 +0100
> 
> Content-Type:
> 
> 
> text/plain
> 
> Parts/Attachments:
> 
> 
> 
> text/plain (17 lines)
> 
> 
> 
> Reply
> 
> Help needed ASAP.
>  
> I am just setting up my new laboratory in Australia (alone at the moment) and 
> already have at least 5 new X-ray structures that need checking and a bit 
> more refinement. High resolution and should not be too much work.
>  
> Therefore, I am looking for a student with experience and/or any help with 
> finalizing the structures (will provide all details to those interested). 
>  
> Happy to add as a co-first author to any manuscripts, as all the wet lab, 
> data collection, and refinements were done by myself ;)
>  
> Cheers. 
>  
>  
>  
> Dr Grant Hansman | Senior Research Fellow
>  
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics 
> (G25) Room 2.56
> T +61 7 5552 9552 | E g.hans...@griffith.edu.au
>  
> griffith.edu.au/institute-glycomics
> 
> Griffith University - CRICOS Provider Number 00233E
> PRIVILEGED - PRIVATE AND CONFIDENTIAL
> This email and any files transmitted with it are intended solely for the use 
> of the addressee(s) and may contain information which is confidential or 
> privileged. If you receive this email and you are not the addressee or 
> responsible for delivery of the email to the addressee(s), please disregard 
> the contents of the email, delete the mail and notify the author immediately.
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Looking for a student and/or help with finalizing new virus spike structures

[Smith Liu]

I am willing to help for your work. Can we communicate for the issue throgh my 
e-mail fenghui...@163.com with fanfeng...@mail.tsinghua.edu.cn cced?
Dr Fenghui Fan






 Replied Message 
| From | Grant Hansman |
| Date | 07/09/2024 12:52 |
| To | CCP4BB@JISCMAIL.AC.UK |
| Cc | |
| Subject | [ccp4bb] Looking for a student and/or help with finalizing new 
virus spike structures |
Help needed ASAP.

I am just setting up my new laboratory in Australia (alone at the moment) and 
already have at least 5 new X-ray structures that need checking and a bit more 
refinement. High resolution and should not be too much work.

Therefore, I am looking for a student with experience and/or any help with 
finalizing the structures (will provide all details to those interested).

Happy to add as a co-first author to any manuscripts, as all the wet lab, data 
collection, and refinements were done by myself ;)

Cheers.



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Re: [ccp4bb] Lattice expansion

[Kay Diederichs]

Hi Charlie,

I don't see a relation between P212121 and F222 that would arise from some kind 
of duplication or halving of axes. These spacegroups have different super- and 
subgroups (see 
https://wiki.uni-konstanz.de/xds/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups).

The volume of the ASU in the (small) F222 cell is 1/8 of the volume of the ASU 
in the (big) P212121 cell (a factor of 1/2 from each of the a and b halvings, 
and another factor of 1/2 from the centering). So there is not even enough 
space for a monomer.

Apparent F222 could arise from twinning of a monoclinic or even triclinic 
packing. Hemihedral twinning "gives you a factor of 2" in the volume of the 
ASU, so that would be 1/4 instead of 1/8. Maybe a monomer could fit. 
Higher-order twinning is possible.

I can think of three things you could do:
1) inspect the predictions very carefully - do they really cover all observed 
reflections, or only every second or so along a and b ? If the latter, you have 
the wrong cell and/or spacegroup.
2) process the data in P1 and do molecular replacement with a monomer. 
3) analyze the crystals on a gel and do mass-spec to make sure they contain the 
protein of interest.

HTH,
Kay

On Mon, 8 Jul 2024 11:07:04 +, Nichols, Charlie  
wrote:

>Hi,
>
>I am trying to recapitulate a published crystallisation system. The published 
>crystal form is P212121 approx cell dimensions 80, 80, 120 // 90, 90, 90 with 
>one trimer in the ASU
>
>We did not get any crystals in the published conditions but have found a new 
>condition giving data to a much higher resolution than the published one but 
>there is a problem...
>
>New crystal form is F222 with approx cell dimensions 40, 40, 120 // 90, 90, 90 
>- this cell is too small to fit one monomer let alone one trimer.
>
>The prep is remarkably clean and there is a high volume of crystals in the 
>drop so unlikely to be a contaminant. I have tried molrep with individual 
>domains in case there has been degradation during crystallisation but this 
>does not look at all promising.
>
>I am wondering, given the almost exact halving of the a/b cell dimensions and 
>almost exact equivalence of the c cell dimension, whether this is a 
>particularly egregious form of twinning where the twin is three 2-fold screw 
>axes to cause an apparent reduction in the unit cell.
>
>Is there a way to expand the data from the current 40, 40, 120 // 90, 90, 90 
>unit cell to the larger 'super-cell' 80, 80, 120 // 90, 90, 90 with four 
>copies of the data to then attempt either molep or just twin refinement with 
>the original published model?
>
>Any comments / help appreciated - NB: I can't share the actual data or even 
>the target as they are confidential client data...
>
>Thanks, take care,
>Charlie Nichols
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Lattice expansion

[Jon Cooper]

Hello, with a=b in both cases, I am sure you have considered tetragonal. I 
remember convincing myself something was F222 when it actually was I422.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 08/07/2024 12:07, Nichols, Charlie  wrote:

> Hi,
>
> I am trying to recapitulate a published crystallisation system. The published 
> crystal form is P212121 approx cell dimensions 80, 80, 120 // 90, 90, 90 with 
> one trimer in the ASU
>
> We did not get any crystals in the published conditions but have found a new 
> condition giving data to a much higher resolution than the published one but 
> there is a problem…
>
> New crystal form is F222 with approx cell dimensions 40, 40, 120 // 90, 90, 
> 90 – this cell is too small to fit one monomer let alone one trimer.
>
> The prep is remarkably clean and there is a high volume of crystals in the 
> drop so unlikely to be a contaminant. I have tried molrep with individual 
> domains in case there has been degradation during crystallisation but this 
> does not look at all promising.
>
> I am wondering, given the almost exact halving of the a/b cell dimensions and 
> almost exact equivalence of the c cell dimension, whether this is a 
> particularly egregious form of twinning where the twin is three 2-fold screw 
> axes to cause an apparent reduction in the unit cell.
>
> Is there a way to expand the data from the current 40, 40, 120 // 90, 90, 90 
> unit cell to the larger ‘super-cell’ 80, 80, 120 // 90, 90, 90 with four 
> copies of the data to then attempt either molep or just twin refinement with 
> the original published model?
>
> Any comments / help appreciated – NB: I can’t share the actual data or even 
> the target as they are confidential client data…
>
> Thanks, take care,
>
> Charlie Nichols
>
> ---
>
> 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] Lattice expansion

[Andy Purkiss]

Hi Charlie,

With xia2 you can try to reprocess and force the spacegroup to be P222 and the 
cell dimensions to be the larger option with the following options:

-spacegroup P212121    
-cell 80,80,120,90,90,90  

This can also be done with other processing pipelines.

I've seen similar cases before and you may find that the P222 cell was found 
but then discarded during the automatic processing as F222 fit just a little 
bit better. If collecting data at Diamond, it is worth uploading the expected 
spacegroup / cell dimensions and then the pipelines will try to process the 
data in the given cell as well as 'ab initio'.

Hope this helps,

Andy



From: CCP4 bulletin board  on behalf of Nichols, Charlie 

Sent: 08 July 2024 12:07
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Lattice expansion


External Sender: Use caution.


Hi,



I am trying to recapitulate a published crystallisation system. The published 
crystal form is P212121 approx cell dimensions 80, 80, 120 // 90, 90, 90 with 
one trimer in the ASU



We did not get any crystals in the published conditions but have found a new 
condition giving data to a much higher resolution than the published one but 
there is a problem…



New crystal form is F222 with approx cell dimensions 40, 40, 120 // 90, 90, 90 
– this cell is too small to fit one monomer let alone one trimer.



The prep is remarkably clean and there is a high volume of crystals in the drop 
so unlikely to be a contaminant. I have tried molrep with individual domains in 
case there has been degradation during crystallisation but this does not look 
at all promising.



I am wondering, given the almost exact halving of the a/b cell dimensions and 
almost exact equivalence of the c cell dimension, whether this is a 
particularly egregious form of twinning where the twin is three 2-fold screw 
axes to cause an apparent reduction in the unit cell.



Is there a way to expand the data from the current 40, 40, 120 // 90, 90, 90 
unit cell to the larger ‘super-cell’ 80, 80, 120 // 90, 90, 90 with four copies 
of the data to then attempt either molep or just twin refinement with the 
original published model?



Any comments / help appreciated – NB: I can’t share the actual data or even the 
target as they are confidential client data…



Thanks, take care,

Charlie Nichols



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Re: [ccp4bb] PDBE - HTTP Status 404?

[Harry Powell]

Ok, it seems to be back again. Maybe the servers had a hangover after 
yesterday’s celebrations…

Harry

> On 5 Jul 2024, at 11:43, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi folks
> 
> https://www.ebi.ac.uk/pdbe
> 
> HTTP Status 404 - Not Found 
> 
> ??
> 
> Harry
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
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Re: [ccp4bb] Imosflm help twinned crystal data

[Jon Cooper]

That's one you made earlier ;-0

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 04/07/2024 20:13, CCP4BB wrote:

> Hi
>
> The best advice I can give if you're new to iMosflm is to work through this 
> tutorial, and feel free to ask questions.
>
> https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/documentation/tutorial.html
>
> Note that I don't work on the project any more so I have to concentrate on 
> the day job - but I can help if you're willing to be a little patient...
>
> Harry
> --
> Dr Harry Powell
>
> On 4 Jul 2024, at 18:42, Marco 
>  wrote:
>
>> Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
>> data, since the autoprocessed data from XDS at the synchotron is not giving 
>> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
>> think the crystal might be twinned however and thus might be making 
>> structural solution difficult for a beginner crystallographer like me. 
>> However an expert in my lab was able to solve the structure with the data 
>> and told me to use imosflm to reprocess the data. They want me to figure 
>> this out on my own with that hint. Is there any tips or resources you can 
>> recommend to help me process my twinned data?
>>
>> Thank you
>>
>> Happy 4th of July!
>>
>> 
>>
>> 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] Imosflm help twinned crystal data

[Jon Cooper]

Oh dear, that sounds like Blue Peter science. I regret though that I haven't 
used mosflm in earnest for a while myself. I do hope someone can be more 
helpful. 

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 04/07/2024 18:42, Marco  
wrote:

>  Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
> data, since the autoprocessed data from XDS at the synchotron is not giving 
> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
> think the crystal might be twinned however and thus might be making 
> structural solution difficult for a beginner crystallographer like me. 
> However an expert in my lab was able to solve the structure with the data and 
> told me to use imosflm to reprocess the data. They want me to figure this out 
> on my own with that hint. Is there any tips or resources you can recommend to 
> help me process my twinned data?
>  
>  Thank you
>  
>  Happy 4th of July!
>  
>  
>  
>  To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Imosflm help twinned crystal data

[CCP4BB]

Hi

The best advice I can give if you're new to iMosflm is to work through this 
tutorial, and feel free to ask questions.

https://www.mrc-lmb.cam.ac.uk/mosflm/imosflm/ver740/documentation/tutorial.html

Note that I don't work on the project any more so I have to concentrate on the 
day job - but I can help if you're willing to be a little patient...

Harry
--
Dr Harry Powell

> On 4 Jul 2024, at 18:42, Marco 
>  wrote:
> 
> Hi all I am trying to use imosflm in ccp4i2 to re-process my diffraction 
> data, since the autoprocessed data from XDS at the synchotron is not giving 
> me a solution. I think the crystal has decent resolution around 2.5-2.6A. I 
> think the crystal might be twinned however and thus might be making 
> structural solution difficult for a beginner crystallographer like me. 
> However an expert in my lab was able to solve the structure with the data and 
> told me to use imosflm to reprocess the data. They want me to figure this out 
> on my own with that hint. Is there any tips or resources you can recommend to 
> help me process my twinned data? 
> 
> Thank you
> 
> Happy 4th of July!
> 
> 
> 
> 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] Tools for identifying possible contaminants

[Deborah Harrus]

Dear Kyle, Clemens, and all,

We use a similar approach at PDB to look for common assemblies, but 
using the center of mass. The item is not yet public though, but if you 
send me the values (that can be calculated using gemmi: 
https://gemmi.readthedocs.io/en/latest/mol.html#model) I can have a 
quick scan though released entries.


Kind regards,

Deborah


On 04/07/2024 10:25, Clemens Vonrhein wrote:

Dear Kyle,

I often like lookint at the crystal.idx file [1] for PDB structures
with very similar cell dimensions ... and then doing some quick MR to
see if one of those sticks out. Easy to fully automate if you have a
local copy of the PDB archive, but something like that (bash)

   cell="30 40 50 90 90 90" # your cell
   maxd=2   # max deviation (A and degree)
   [ ! -f crystal.idx ] && wget -q 
https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
   awk -v cell="$cell" -v maxd=$maxd 'BEGIN{
 i=split(cell,c)
   }
   /CRYST1/{
 for(i=1;i<=6;i++) {
   d=c[i]-$(i+2);if(d<0)d=-d
   if(d>maxd)next
 }
 print
   }' crystal.idx

would give you a first listing ...

Cheers

Clemens

[1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx


On Wed, Jul 03, 2024 at 03:54:20PM +, Kyle Gregory wrote:

Dear all,

We have a unit cell that is too small for our expected protein and suspect we 
have crystalised a contaminant.

Does anyone have any recommendations on which tools we could use to identify 
the possible contaminant? I've tried SIMAD on ccp4cloud and it doesn't suggest 
anything reasonable.

Kind regards,
Kyle



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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Eleanor Dodson]

I Am thinking about this problem re a set of four carbohydrate binding
proteins - all isomorphous but with different Ligands and weird solvent
features..
first task was to get all sets with same indexing convention!
(SoacegroupP65) That can be done at the data processing stage by giving one
as the reference set.
Then I wanted all the models to be on the same origin and symmetry to make
comparisons easier. You can do molecular replacement fir each then use the
task “match model to reference” but it is easier to just start refinement
with the basic first model then correct and refine the new one as the maps
indicate..
maybe it is enough then to just look at all naps in COOT together but I
want to do an Fobs1 - Fobs2 difference map..
There is a ccp4i2 task to compare datasets using scaleit to match them.
That gives useful analysis of differences and then If you have calculated
phases for your best model then you can do such a difference nap. It
certainly shows up features which I expect to be different
However there seems to be a bug in the cmapcoeff version for this.. The old
*fft* script in ccp4i works OK with that input.
Eleanor

On Sat, 15 Jun 2024 at 13:53, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Comparing maps sounds justi. A like the sort of thing the Uppsala suite
> did. Maybe you can find an old binary for mapman or mapman2(?) or compile
> it from Martin Winn's github page. The closest I can find is EDSTATS which
> I think is in the old ccp4 gui.
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>
>  Original Message 
>
> On 14/06/2024 20:58, Matt Mcleod wrote:
>
> I should clarify.  I am mostly concerned about the electron density map.
>
> I want to make sure that I can most closely compare the maps from two
> different quality structures, rather than the datasets themselves via CC1/2
> or other metrics.  This is more so for interpreting structural changes.
>
> For example, if there is sparse density for some particular thing
> indicating partial occupancy, how can I compare those two maps.  So for
> low-resolution datasets, maybe there is less density but is that because of
> data quality or because in that dataset there is a lower occupancy through
> some meaningful structural change (compared to higher resolution/better
> data)?
>
> On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am wondering what the best practice is to compare datasets that are of
>> the same protein but different quality, for instance 2 vs. 3 A.
>>
>> I know that truncating the structures to the same resolution bin is
>> alright, but the data quality in the lower resolution bins are also not the
>> same.  Is there a way to "inject" noise into the data such that the bins
>> are more similar?
>>
>> These datasets cannot be recollected at higher resolution since they are
>> collected at increasingly high pressure, and the resolution change is
>> anticorrelated with the pressure; no way to get around crystal stability.
>>
>> Any suggestions are appreciated,
>> Matt
>>
>> 
>>
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>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
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>
>
> --
> *Matthew Jordan McLeod, PhD*
> *Post-Doctoral Fellow - Cornell University*
>
>
>
>
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Re: [ccp4bb] Tools for identifying possible contaminants

[Eleanor Dodson]

In fact I believe that is what the SIMBAD script does - searches the PDB
archive first for cell dimensions, and only then checks possible MR
matches..

On Thu, 4 Jul 2024 at 10:26, Clemens Vonrhein <
daef624adb06-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Kyle,
>
> I often like lookint at the crystal.idx file [1] for PDB structures
> with very similar cell dimensions ... and then doing some quick MR to
> see if one of those sticks out. Easy to fully automate if you have a
> local copy of the PDB archive, but something like that (bash)
>
>   cell="30 40 50 90 90 90" # your cell
>   maxd=2   # max deviation (A and degree)
>   [ ! -f crystal.idx ] && wget -q
> https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
>   awk -v cell="$cell" -v maxd=$maxd 'BEGIN{
> i=split(cell,c)
>   }
>   /CRYST1/{
> for(i=1;i<=6;i++) {
>   d=c[i]-$(i+2);if(d<0)d=-d
>   if(d>maxd)next
> }
> print
>   }' crystal.idx
>
> would give you a first listing ...
>
> Cheers
>
> Clemens
>
> [1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
>
>
> On Wed, Jul 03, 2024 at 03:54:20PM +, Kyle Gregory wrote:
> > Dear all,
> >
> > We have a unit cell that is too small for our expected protein and
> suspect we have crystalised a contaminant.
> >
> > Does anyone have any recommendations on which tools we could use to
> identify the possible contaminant? I've tried SIMAD on ccp4cloud and it
> doesn't suggest anything reasonable.
> >
> > Kind regards,
> > Kyle
> >
> > 
> >
> > 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/
>
> --
>
> *--
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> * Global Phasing Ltd., Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK   www.globalphasing.com
> *--
>
> 
>
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Re: [ccp4bb] Tools for identifying possible contaminants

[Clemens Vonrhein]

Dear Kyle,

I often like lookint at the crystal.idx file [1] for PDB structures
with very similar cell dimensions ... and then doing some quick MR to
see if one of those sticks out. Easy to fully automate if you have a
local copy of the PDB archive, but something like that (bash)

  cell="30 40 50 90 90 90" # your cell
  maxd=2   # max deviation (A and degree)
  [ ! -f crystal.idx ] && wget -q 
https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx
  awk -v cell="$cell" -v maxd=$maxd 'BEGIN{
i=split(cell,c)
  }
  /CRYST1/{
for(i=1;i<=6;i++) {
  d=c[i]-$(i+2);if(d<0)d=-d
  if(d>maxd)next
}
print
  }' crystal.idx

would give you a first listing ...

Cheers

Clemens

[1] https://files.wwpdb.org/pub/pdb/derived_data/index/crystal.idx


On Wed, Jul 03, 2024 at 03:54:20PM +, Kyle Gregory wrote:
> Dear all,
> 
> We have a unit cell that is too small for our expected protein and suspect we 
> have crystalised a contaminant.
> 
> Does anyone have any recommendations on which tools we could use to identify 
> the possible contaminant? I've tried SIMAD on ccp4cloud and it doesn't 
> suggest anything reasonable.
> 
> Kind regards,
> Kyle
> 
> 
> 
> 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 
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-- 

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



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Re: [ccp4bb] Off topic ; how to remove fluorescein from superdex increase

[Jurgen Bosch]

Have you tried Guanidinium chloride?

Jürgen 

> On Jul 3, 2024, at 1:22 PM, Daniele de Sanctis  wrote:
> 
> Hi Flavio
> 
> I’d suggest to contact Regenfix 
> https://www.regenfix.eu/
> 
> Usually they give you back a column better than the original one completed 
> with an experimental calibration curve.
> 
> Cheers 
> 
> Daniele
> 
> 
> 
> On Wed 3 Jul 2024 at 18:56, Nicholas Clark 
>  > wrote:
>> Hi Flavio,
>> 
>> I’d recommend reaching out to Cytiva directly 
>> (scientificsupport...@cytiva.com ). 
>> We had an issue with oxidized metal on our S200 and they were able to 
>> provide useful suggestions (plus side is, you know what they suggest won’t 
>> ruin the resin).
>> 
>> Best,
>> 
>> Nick Clark
>> 
>> Nicholas D. Clark, PhD (He/Him)
>> University at Buffalo
>> Department of Structural Biology
>> Jacob's School of Medicine & Biomedical Sciences
>> 955 Main Street 
>> 
>> Buffalo, NY 14203 
>> 
>> 
>> 
>> On Wed, Jul 3, 2024 at 12:01 PM Flavio Di Pisa > > wrote:
>>> Dear community,
>>> do you have any advice on how to remove the fluorescein from a superdex 200 
>>> increase?
>>> Thank you
>>> Flavio.
>>> 
>>> 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] Off topic ; how to remove fluorescein from superdex increase

[Daniele de Sanctis]

Hi Flavio

I’d suggest to contact Regenfix
https://www.regenfix.eu/

Usually they give you back a column better than the original one completed
with an experimental calibration curve.

Cheers

Daniele



On Wed 3 Jul 2024 at 18:56, Nicholas Clark <
b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi Flavio,
>
> I’d recommend reaching out to Cytiva directly (
> scientificsupport...@cytiva.com). We had an issue with oxidized metal on
> our S200 and they were able to provide useful suggestions (plus side is,
> you know what they suggest won’t ruin the resin).
>
> Best,
>
> Nick Clark
>
> Nicholas D. Clark, PhD (He/Him)
> University at Buffalo
> Department of Structural Biology
> Jacob's School of Medicine & Biomedical Sciences
> 955 Main Street
> 
> Buffalo, NY 14203
> 
>
>
> On Wed, Jul 3, 2024 at 12:01 PM Flavio Di Pisa  wrote:
>
>> Dear community,
>> do you have any advice on how to remove the fluorescein from a superdex
>> 200 increase?
>> Thank you
>> Flavio.
>>
>> --
>>
>> 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] Off topic ; how to remove fluorescein from superdex increase

[Nicholas Clark]

Hi Flavio,

I’d recommend reaching out to Cytiva directly (
scientificsupport...@cytiva.com). We had an issue with oxidized metal on
our S200 and they were able to provide useful suggestions (plus side is,
you know what they suggest won’t ruin the resin).

Best,

Nick Clark

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


On Wed, Jul 3, 2024 at 12:01 PM Flavio Di Pisa  wrote:

> Dear community,
> do you have any advice on how to remove the fluorescein from a superdex
> 200 increase?
> Thank you
> Flavio.
>
> --
>
> 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] Tools for identifying possible contaminants

[Mike S]

I think this may do the contaminant search you are looking for.
ContaMiner (kaust.edu.sa)


Best,
Mike

On Wed, Jul 3, 2024 at 12:04 PM Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>
> We have a unit cell that is too small for our expected protein and suspect
> we have crystalised a contaminant.
>
> Does anyone have any recommendations on which tools we could use to
> identify the possible contaminant? I've tried SIMAD on ccp4cloud and it
> doesn't suggest anything reasonable.
>
> Kind regards,
> Kyle
>
> --
>
> 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] ATP analogues

[Matthew BOWLER]

Dear Reza,

the stability of these complexes is variable and depends on many factors 
including your protein, the pH of the buffer etc. I would recommend 
aluminium fluoride as the most stable (below pH8) as it is present in 
solution and has a the highest charge to size ratio so binds tightly in 
the active site. However, if your goal is to study the ground state use 
BeF3-. We have a preprint out that goes into much more detail - see 
https://www.biorxiv.org/content/10.1101/2024.03.25.586559v1.full



Best wishes, Matt



On 03/07/2024 16:58, Reza Khayat wrote:

Hi,

Sorry for the non crystallography question. We need to make some ATP 
analogues (ADP BeFx, ADP MgF3, and ADP AlFx). I have attained 
protocols from manuscripts for making these; however, am concerned 
that something important in the protocol may be lacking. Also, how 
stable are these samples? Thanks.


Best wishes,
Reza

Reza Khayat, PhD
City College of New York
Associate Professor
Department of Chemistry and Biochemistry
Co-Director NIH G-RISE program




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===
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===



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Re: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

[Xu, Qingping]

This is a reminder that we are still accepting applications for the upcoming 
CCP4@APS workshop below. Potential students, esp those from outside the US, are 
encouraged to submit their applications asap.

This Message Is From an External Sender
This message came from outside your organization.


Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS),
Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All
details can be found at the school website:
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-2024/index.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RU9QBjAs8$.
 This will be our first
work post the APS-U upgrade.


Dates: October 28 through November 4, 2024

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near

Chicago), Illinois, USA

The school comprises two parts: data collection (provisional pending APS
availability) workshop and crystallographic computing workshop. Data
collection workshop includes beamline training, data collection on
GM/CA@APS beamlines, and data processing, using only the participants'
crystals. Crystallographic computation workshop will feature many modern
crystallographic software packages taught by authors and other experts.
This workshop will also introduce elements of CryoEM. The daily schedule
will be organized in three sections – lectures, tutorials, and hands-on
(interactive trouble-shooting of the technical difficulties the
participants face in their projects). We have had considerable success
resolving these problems in past years, attested by resulting
publications (see
https://urldefense.us/v3/__http://www.ccp4.ac.uk/schools/APS-school/publications.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUPTfq2LA$).
 A draft
program can be found at the School website.

Applicants: The workshop strongly encourages students who need expert
help with difficulties/challenges in their own projects. Graduate
students, postdoctoral researchers and early-career faculty, along with
commercial/industrial researchers are encouraged to apply. Only about 20
applicants will be selected for participation.

Application: Application deadline is  August 31st, 2024. To apply,
visit  
https://urldefense.us/v3/__https://www.ccp4.ac.uk/schools/APS-2024/application.php__;!!G_uCfscf7eWS!aOleuXi7N-9nfMCKB4-O6nKb0FJxs_pyLJVeg_xPlgECCN90m6Q-s1604W4l5R5HMh3KD_g2-jQoUfLG0Rb7c0RUhRwAcxE$

Fees: There is a $500 participation fee for the selected academic
students and $1500 for industrial researchers. No credit card will be
required for registration, students who are selected to participate will
be contacted to pay. The students will be responsible for their
transportation and lodging. The workshop organizers can assist in making
lodging reservations at the Argonne Guest House. The workshop will cover
all other expenses (including meals).


We hope to see you at the school.

Charles, Andrey, Garib and Qingping



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From: CCP4 bulletin board  on behalf of Qingping Xu 
<292fcbdb7ebe-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, April 8, 2024 1:26 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

This Message Is From an External Sender
This message came from outside your organization.


Dear Colleagues,

We are pleased to announce the 16th annual CCP4/APS crystallographic
school “From data collection to structure refinement and beyond” will be
held on Oct 28th to Nov 4th, 2024 at the Advanced Photon Source (APS),
Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All
details can be found at the school website:

Re: [ccp4bb] Computations Crystallography Newsletter (CCN) Submissions

[Nigel Moriarty]

Hi all

I was sure I edited the submission date to 22 JUL 2024 but the evidence is
to the contrary.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Mon, Jul 1, 2024 at 10:55 AM Nigel Moriarty  wrote:

> Folks
>
> The deadline for submissions to the Computational Crystallography
> Newsletter (CCN) is 22 JAN 2024. Please consider writing an article of
> general interest to the community.
> The Computational Crystallography Newsletter (CCN) is an electronic
> newsletter for structural biologists, and is published online every 6
> months. Feature articles, meeting announcements and reports can be
> submitted to me at any time for consideration. Submission of text by email
> or word-processing files using the CCN templates is requested.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Email : nwmoria...@lbl.gov
> Web  : CCI.LBL.gov
> ORCID : orcid.org/-0001-8857-9464
>



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Re: [ccp4bb] minor off topic protein symmetry

[Artem Evdokimov]

It is possible that the following tetramer displays the features you seek:

https://www.rcsb.org/structure/6v1v

You will notice that this is P1. When I solved it, I had at first some
trouble recognizing why this molecule does not have a P4 (I am slow, I
guess) but then it dawned on me :) It displays one of the cutest symmetry
transitions that I've seen so far.

Artem

- Cosmic Cats approve of this message


On Thu, Jun 27, 2024 at 8:46 AM Andrew Lovering 
wrote:

> Dear wise list,
>
>
>
> I have a question regarding protein oligomers that have multiple,
> differing axes of symmetry – stimulated by some perplexing but likely real
> Alphafold models.
>
>
>
> I think it’s the protein equivalent of this old chestnut:
> https://en.wikipedia.org/wiki/Three_utilities_problem
>
>
>
> Consider a trimeric fibre (perhaps collagen a good starting example) – it
> can have global 3-fold symmetry, and if it breaks from this, it is then
> able to “re-obey” this symmetry later on, but that axis is approximately
> the same as the starting one. I.e. a long winding rope with a kink in the
> middle, and the protein doesn’t have to do much to accommodate this.
>
>
>
> What happens when a long protein has multiple, dissimilar axes of
> symmetry? I.e. perhaps a trimer with the start and end on the same axis,
> but the middle domain sits ~90 degrees to this (and is also a 3-fold
> arrangement of chains A,B & C). I think I’d be correct in assuming that all
> 3 chains cannot have the same conformation – is this true?
>
> I’d argue that the protein has to unwind a little at the junctions and
> each chain takes a different path in space when migrating from axis 1> axis
> 2> back to axis 1? (think of 1 as up/down, 2 as left/right). This is
> because as each chain leaves the centre of mass of axis 1, it is a
> different distance away from the centre of mass of axis 2….?
>
>
>
> I hope that makes some sense!
>
>
>
> So my question is, does anyone have an example PDB that does something
> similar, and were they able to trace the different chains, demonstrating
> the different conformations.
>
>
>
> Thanks in advance - Andy
>
> --
>
> 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] Good electron density but poor affinity

[Tanner, John]

The refined crystallographic occupancy (sort of a measure of electron density 
quality) has been related to the ligand binding constant. In this study, they 
determined several structures of a protein with different concentrations of the 
ligand. The binding constant was estimated from a plot of the refined Q versus 
ligand concentration.

https://pubmed.ncbi.nlm.nih.gov/11180378/


--
John J. Tanner
Professor of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
573-884-1280
tanne...@missouri.edu



From: CCP4 bulletin board  on behalf of Armando Albert 

Date: Thursday, June 27, 2024 at 7:52 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Good electron density but poor affinity
WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.

Dear all,
Is there any study that analyzes the relationship between the quality of the 
electron density of a ligand and its affinity?
Armando


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Re: [ccp4bb] mystery blob!

[Eleanor Dodson]

Thank you all for the ideas!

On Wed, 26 Jun 2024 at 16:49, MARCHOT Pascale 
wrote:

>
> *One of these green little gosts?*
>
> *P *
>
> --
> *De :* CCP4 bulletin board  de la part de Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Envoyé :* mercredi 26 juin 2024 17:09
> *À :* CCP4BB@JISCMAIL.AC.UK
> *Objet :* [ccp4bb] mystery blob!
>
>
> Ce mail provient de l'extérieur, restons vigilants
> ANY ideas what this could be
>
>
> --
>
> 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] mystery blob!

[Yves Muller]

a HEPES molecule?

Regards,

Yves

--

Prof. Yves Muller   Phone: +49-(0)-9131-8523082, 8523081
Lehrstuhl fuer BiotechnikFAX:   +49-(0)-9131-8523080
www.biotechnik.nat.fau.de
Department Biologie
Friedrich-Alexander-Universität, Erlangen-Nuernberg
Im MVC, Henkestrasse 91, D-91052 Erlangen




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Re: [ccp4bb] mystery blob!

[Tom Huxford]

Dear Eleanor,

Perhaps a PMSF-EG adduct?

Tom Huxford.

==
Tom Huxford
Structural Biochemistry Laboratory
Department of Chemistry & Biochemistry
San Diego State University
(619) 594-1606

> On Jun 26, 2024, at 8:09 AM, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> ANY ideas what this could be
> 
> 
> 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] CCP4 Cloud Server Structure Prediction Task Unavailable

[YASH MISRA PHD222012]

Dear Harry,

Thank you for your email and the information regarding the CCP4 Cloud
server. It was really helpful.

On Wed, Jun 26, 2024 at 2:36 PM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi
>
> You probably need to try again later...
>
> It looks to me as if the CCP4 Cloud server (for “remote”) is down for some
> reason - I just tried to run it and I get a pop-up that says “CCP4 Cloud
> Maintenance”, that includes the text “failed to connect”.
>
> I think that the “structure prediction” task is not available for CCP4
> Cloud Desktop unless you have AlphaFold set up to run locally on your
> machine; for most users, this is not very likely.
>
> Generally, though, I’ve found that using CCP4 Cloud is by far the easiest
> way to run AlphaFold predictions (rather than for downloading previously
> predicted models from the DB).
>
> Harry
>
> > On 26 Jun 2024, at 06:00, YASH MISRA PHD222012 <
> yashmisr...@iisertvm.ac.in> wrote:
> >
> > Dear all,
> >
> > Can someone help me with this?
> >
> > Until yesterday it was working fine but today when I tried running this
> task I am getting the following error. I tried accessing this task via.
> https://cloud.ccp4.ac.uk/ using my Windows system as well as LInux but to
> no avail.
> >
> > 
> >
> > I also tried using the CCP4 Cloud Desktop but it showed me the following
> error:
> >
> > 
> >
> > I am not sure which software to install for the latter.
> >
> > Any assistance would be appreciated.
> >
> > Thank you.
> >
> > Kind regards
> >
> > Yash Misra
> > Ph.D. Scholar
> > Dr. R. Natesh Lab
> > School of Biology
> > Indian Institute of Science Education and Research- Thiruvananthapuram
> > Kerala
> > INDIA
> >
> > 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 https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Thank you.

*Kind regards*


*Yash Misra*
*Ph.D. Scholar*

*Dr. R. Natesh Lab*
*School of Biology*

*Indian Institute of Science Education and Research- Thiruvananthapuram*

*Kerala*
*INDIA*



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Re: [ccp4bb] CCP4 Cloud Server Structure Prediction Task Unavailable

[Harry Powell]

Hi

You probably need to try again later...

It looks to me as if the CCP4 Cloud server (for “remote”) is down for some 
reason - I just tried to run it and I get a pop-up that says “CCP4 Cloud 
Maintenance”, that includes the text “failed to connect”.

I think that the “structure prediction” task is not available for CCP4 Cloud 
Desktop unless you have AlphaFold set up to run locally on your machine; for 
most users, this is not very likely.

Generally, though, I’ve found that using CCP4 Cloud is by far the easiest way 
to run AlphaFold predictions (rather than for downloading previously predicted 
models from the DB).

Harry

> On 26 Jun 2024, at 06:00, YASH MISRA PHD222012  
> wrote:
> 
> Dear all,
> 
> Can someone help me with this?
> 
> Until yesterday it was working fine but today when I tried running this task 
> I am getting the following error. I tried accessing this task via. 
> https://cloud.ccp4.ac.uk/ using my Windows system as well as LInux but to no 
> avail. 
> 
> 
> 
> I also tried using the CCP4 Cloud Desktop but it showed me the following 
> error:
> 
> 
> 
> I am not sure which software to install for the latter.
> 
> Any assistance would be appreciated.
> 
> Thank you.
> 
> Kind regards
> 
> Yash Misra
> Ph.D. Scholar
> Dr. R. Natesh Lab
> School of Biology
> Indian Institute of Science Education and Research- Thiruvananthapuram
> Kerala
> INDIA
>  
> 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] List of 3-letter codes of modified amino acids

[Marcus Bage]

Yes, having recently gone through most of the protein modification data 
currently in the archive, the PDB biocurators have overall been very 
consistent with the handling of protein modifications. Despite this, 
inconsistencies have accumulated over the years. In the current project, 
we are adding new annotation and detailed documentation to support the 
future biocuration of new protein modifications. We hope that this will 
ensure consistency is maintained in the future.


Best,
Marcus

On 24/06/2024 17:32, Frances C. Bernstein wrote:
For those who do not know, I worked on data processing for the PDB 
from 1974 to 1998 (entries 15 to ~9000) and we tried to be consistent 
in representing small modifications to amino acids: modified amino 
acid vs. standard amino acid plus het group.  With the then lack of 
software tools we struggled to remember whether we had encountered a 
similar case before.  And there is the additional issue to consider of 
how the depositor views the modification and discusses it in their 
publications.  I am glad to know that the PDB will be standardizing 
the data representation of these cases.


    Frances

On 2024-06-24 12:11, Marcus Bage wrote:

Hi Frances,

This is one of the central issues being addressed as part of the 
protein modifications project.


When the PDB archive is updated as part of the project rollout, all 
protein modifications will be grouped into distinct categories of 
modification. The category they fall in determines how they will be 
handled throughout the archive.


In general, small, well-described protein modifications will be 
handled as part of the modified amino acid group. For example 
phosphorylations, methylations and acetylations.


Modifications that that are large, branched or that link multiple 
protein residues will be handled as linked het groups. For example 
carbohydrates, hemes, lipids and crosslinkers.


This approach will make it easier to ensure that all modification 
groups are handled in a single consistent way throughout the archive. 
A significant effort is being made to standardise protein 
modifications in all existing entries to ensure that this will be the 
case for the whole archive.


For more detailed information about this project please see:
github.com/wwPDB/protein-modification-extension

Kind Regards,
Marcus

On 24/06/2024 16:44, f...@marbuta.pair.com wrote:
Would it be possible for the PDB to explain the distinction in 
representation between the case of a modified amino acid and the 
case of additional atoms bound to the side chain of a standard amino 
acid.  If it is a standard amino acid will the extra atom(s) always 
be represented as a het group?  Is the PDB consistent through all 
entries in such a case?


   Frances Bernstein

On 2024-06-24 11:03, Marcus Bage wrote:

Hi everyone,

Last year wwPDB standardised the backbone atom names for all 
residues that are part of a polypeptide sequence within the PDB 
archive. A full list of all chemical components affected can be 
found at:

github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard 
peptide residues within the PDB archive. It was last updated in 
August 2023.


wwPDB is in the process of standardising and enriching all protein 
modification data in the PDB archive. As part of this, all modified 
peptide residues will have data added to their CCD definition file 
to describe in what way the residue is modified. For example, the 
3-letter code SEP, will have the information to state that it is 
the phosphorylation of serine. Once this information is released it 
will be considerably easier to access such information in the archive.


A detailed description of the changes being made as part of the PTM 
standardisation project can be found at:

github.com/wwPDB/protein-modification-extension

Kind regards,
Marcus

On 24/06/2024 15:21, Harry Powell wrote:

Hi folks

“Can of worms” is how this could be described!

 From various different sources (many thanks Paul, Mitch, Robbie) 
I have now managed to obtain (inter alia) lists of 31, 189, 863 
and 916 modified amino acids - and there are other, longer (and 
possibly shorter and equimetric [is that even a word?] lists that 
I could create if I want to be more comprehensive! It’s certainly 
_possible_ that some of the members of an individual list are 
duplicates, but for my current purposes these should suffice 
nearly all the time (and for those cases where the list falls 
short, I would expect people to raise the issue directly with me…)


Once more, I knew this would be the place to ask!

Harry

On 24 Jun 2024, at 13:40, Robbie Joosten 
 wrote:


Hi Harry,

A BSc student in our lab just had a look at this. Here is the 
list of mappings pdb-redo uses: 
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
(second to last loop).


Cheers,
Robbie

pdb-redo-main/tools/pdb-redo-data.cif at trunk · 

Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Frances C. Bernstein]

For those who do not know, I worked on data processing for the PDB from 
1974 to 1998 (entries 15 to ~9000) and we tried to be consistent in 
representing small modifications to amino acids: modified amino acid vs. 
standard amino acid plus het group.  With the then lack of software 
tools we struggled to remember whether we had encountered a similar case 
before.  And there is the additional issue to consider of how the 
depositor views the modification and discusses it in their publications. 
 I am glad to know that the PDB will be standardizing the data 
representation of these cases.


Frances

On 2024-06-24 12:11, Marcus Bage wrote:

Hi Frances,

This is one of the central issues being addressed as part of the 
protein modifications project.


When the PDB archive is updated as part of the project rollout, all 
protein modifications will be grouped into distinct categories of 
modification. The category they fall in determines how they will be 
handled throughout the archive.


In general, small, well-described protein modifications will be handled 
as part of the modified amino acid group. For example phosphorylations, 
methylations and acetylations.


Modifications that that are large, branched or that link multiple 
protein residues will be handled as linked het groups. For example 
carbohydrates, hemes, lipids and crosslinkers.


This approach will make it easier to ensure that all modification 
groups are handled in a single consistent way throughout the archive. A 
significant effort is being made to standardise protein modifications 
in all existing entries to ensure that this will be the case for the 
whole archive.


For more detailed information about this project please see:
github.com/wwPDB/protein-modification-extension

Kind Regards,
Marcus

On 24/06/2024 16:44, f...@marbuta.pair.com wrote:
Would it be possible for the PDB to explain the distinction in 
representation between the case of a modified amino acid and the case 
of additional atoms bound to the side chain of a standard amino acid.  
If it is a standard amino acid will the extra atom(s) always be 
represented as a het group?  Is the PDB consistent through all entries 
in such a case?


   Frances Bernstein

On 2024-06-24 11:03, Marcus Bage wrote:

Hi everyone,

Last year wwPDB standardised the backbone atom names for all residues 
that are part of a polypeptide sequence within the PDB archive. A 
full list of all chemical components affected can be found at:

github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard 
peptide residues within the PDB archive. It was last updated in 
August 2023.


wwPDB is in the process of standardising and enriching all protein 
modification data in the PDB archive. As part of this, all modified 
peptide residues will have data added to their CCD definition file to 
describe in what way the residue is modified. For example, the 
3-letter code SEP, will have the information to state that it is the 
phosphorylation of serine. Once this information is released it will 
be considerably easier to access such information in the archive.


A detailed description of the changes being made as part of the PTM 
standardisation project can be found at:

github.com/wwPDB/protein-modification-extension

Kind regards,
Marcus

On 24/06/2024 15:21, Harry Powell wrote:

Hi folks

“Can of worms” is how this could be described!

 From various different sources (many thanks Paul, Mitch, Robbie) I 
have now managed to obtain (inter alia) lists of 31, 189, 863 and 
916 modified amino acids - and there are other, longer (and possibly 
shorter and equimetric [is that even a word?] lists that I could 
create if I want to be more comprehensive! It’s certainly _possible_ 
that some of the members of an individual list are duplicates, but 
for my current purposes these should suffice nearly all the time 
(and for those cases where the list falls short, I would expect 
people to raise the issue directly with me…)


Once more, I knew this would be the place to ask!

Harry

On 24 Jun 2024, at 13:40, Robbie Joosten 
 wrote:


Hi Harry,

A BSc student in our lab just had a look at this. Here is the list 
of mappings pdb-redo uses: 
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
(second to last loop).


Cheers,
Robbie

pdb-redo-main/tools/pdb-redo-data.cif at trunk · 
PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to 
PDB-REDO/pdb-redo-main development by creating an account on 
GitHub.

github.com

From: CCP4 bulletin board  on behalf of 
Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>

Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] List of 3-letter codes of modified amino acids
  Hi

An internet search doesn’t yield an obvious list of these (I did 
find a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are 
293, but the 

Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Marcus Bage]

Hi Frances,

This is one of the central issues being addressed as part of the protein 
modifications project.


When the PDB archive is updated as part of the project rollout, all 
protein modifications will be grouped into distinct categories of 
modification. The category they fall in determines how they will be 
handled throughout the archive.


In general, small, well-described protein modifications will be handled 
as part of the modified amino acid group. For example phosphorylations, 
methylations and acetylations.


Modifications that that are large, branched or that link multiple 
protein residues will be handled as linked het groups. For example 
carbohydrates, hemes, lipids and crosslinkers.


This approach will make it easier to ensure that all modification groups 
are handled in a single consistent way throughout the archive. A 
significant effort is being made to standardise protein modifications in 
all existing entries to ensure that this will be the case for the whole 
archive.


For more detailed information about this project please see:
github.com/wwPDB/protein-modification-extension

Kind Regards,
Marcus

On 24/06/2024 16:44, f...@marbuta.pair.com wrote:
Would it be possible for the PDB to explain the distinction in 
representation between the case of a modified amino acid and the case 
of additional atoms bound to the side chain of a standard amino acid.  
If it is a standard amino acid will the extra atom(s) always be 
represented as a het group?  Is the PDB consistent through all entries 
in such a case?


   Frances Bernstein

On 2024-06-24 11:03, Marcus Bage wrote:

Hi everyone,

Last year wwPDB standardised the backbone atom names for all residues 
that are part of a polypeptide sequence within the PDB archive. A 
full list of all chemical components affected can be found at:

github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard 
peptide residues within the PDB archive. It was last updated in 
August 2023.


wwPDB is in the process of standardising and enriching all protein 
modification data in the PDB archive. As part of this, all modified 
peptide residues will have data added to their CCD definition file to 
describe in what way the residue is modified. For example, the 
3-letter code SEP, will have the information to state that it is the 
phosphorylation of serine. Once this information is released it will 
be considerably easier to access such information in the archive.


A detailed description of the changes being made as part of the PTM 
standardisation project can be found at:

github.com/wwPDB/protein-modification-extension

Kind regards,
Marcus

On 24/06/2024 15:21, Harry Powell wrote:

Hi folks

“Can of worms” is how this could be described!

 From various different sources (many thanks Paul, Mitch, Robbie) I 
have now managed to obtain (inter alia) lists of 31, 189, 863 and 
916 modified amino acids - and there are other, longer (and possibly 
shorter and equimetric [is that even a word?] lists that I could 
create if I want to be more comprehensive! It’s certainly _possible_ 
that some of the members of an individual list are duplicates, but 
for my current purposes these should suffice nearly all the time 
(and for those cases where the list falls short, I would expect 
people to raise the issue directly with me…)


Once more, I knew this would be the place to ask!

Harry

On 24 Jun 2024, at 13:40, Robbie Joosten 
 wrote:


Hi Harry,

A BSc student in our lab just had a look at this. Here is the list 
of mappings pdb-redo uses: 
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
(second to last loop).


Cheers,
Robbie

pdb-redo-main/tools/pdb-redo-data.cif at trunk · 
PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to 
PDB-REDO/pdb-redo-main development by creating an account on GitHub.

github.com

From: CCP4 bulletin board  on behalf of 
Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>

Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] List of 3-letter codes of modified amino acids
  Hi

An internet search doesn’t yield an obvious list of these (I did 
find a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are 
293, but the link included appears to be dead - 
http://deposit.pdb.org/hetdictionary.txt).


I’m almost convinced that this has been asked here previously (if 
not recently), but a quick search through ccp4bb postings has not 
revealed it to me.


Can anyone help?

Harry
 



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 
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Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Frances C. Bernstein]

Would it be possible for the PDB to explain the distinction in 
representation between the case of a modified amino acid and the case of 
additional atoms bound to the side chain of a standard amino acid.  If 
it is a standard amino acid will the extra atom(s) always be represented 
as a het group?  Is the PDB consistent through all entries in such a 
case?


   Frances Bernstein

On 2024-06-24 11:03, Marcus Bage wrote:

Hi everyone,

Last year wwPDB standardised the backbone atom names for all residues 
that are part of a polypeptide sequence within the PDB archive. A full 
list of all chemical components affected can be found at:

github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard 
peptide residues within the PDB archive. It was last updated in August 
2023.


wwPDB is in the process of standardising and enriching all protein 
modification data in the PDB archive. As part of this, all modified 
peptide residues will have data added to their CCD definition file to 
describe in what way the residue is modified. For example, the 3-letter 
code SEP, will have the information to state that it is the 
phosphorylation of serine. Once this information is released it will be 
considerably easier to access such information in the archive.


A detailed description of the changes being made as part of the PTM 
standardisation project can be found at:

github.com/wwPDB/protein-modification-extension

Kind regards,
Marcus

On 24/06/2024 15:21, Harry Powell wrote:

Hi folks

“Can of worms” is how this could be described!

 From various different sources (many thanks Paul, Mitch, Robbie) I 
have now managed to obtain (inter alia) lists of 31, 189, 863 and 916 
modified amino acids - and there are other, longer (and possibly 
shorter and equimetric [is that even a word?] lists that I could 
create if I want to be more comprehensive! It’s certainly _possible_ 
that some of the members of an individual list are duplicates, but for 
my current purposes these should suffice nearly all the time (and for 
those cases where the list falls short, I would expect people to raise 
the issue directly with me…)


Once more, I knew this would be the place to ask!

Harry

On 24 Jun 2024, at 13:40, Robbie Joosten  
wrote:


Hi Harry,

A BSc student in our lab just had a look at this. Here is the list of 
mappings pdb-redo uses: 
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
(second to last loop).


Cheers,
Robbie

pdb-redo-main/tools/pdb-redo-data.cif at trunk · 
PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to 
PDB-REDO/pdb-redo-main development by creating an account on GitHub.

github.com

From: CCP4 bulletin board  on behalf of Harry 
Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk>

Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] List of 3-letter codes of modified amino acids
  Hi

An internet search doesn’t yield an obvious list of these (I did find 
a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but 
the link included appears to be dead - 
http://deposit.pdb.org/hetdictionary.txt).


I’m almost convinced that this has been asked here previously (if not 
recently), but a quick search through ccp4bb postings has not 
revealed it to me.


Can anyone help?

Harry


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/



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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 
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To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Marcus Bage]

Hi everyone,

Last year wwPDB standardised the backbone atom names for all residues 
that are part of a polypeptide sequence within the PDB archive. A full 
list of all chemical components affected can be found at:

github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard 
peptide residues within the PDB archive. It was last updated in August 2023.


wwPDB is in the process of standardising and enriching all protein 
modification data in the PDB archive. As part of this, all modified 
peptide residues will have data added to their CCD definition file to 
describe in what way the residue is modified. For example, the 3-letter 
code SEP, will have the information to state that it is the 
phosphorylation of serine. Once this information is released it will be 
considerably easier to access such information in the archive.


A detailed description of the changes being made as part of the PTM 
standardisation project can be found at:

github.com/wwPDB/protein-modification-extension

Kind regards,
Marcus

On 24/06/2024 15:21, Harry Powell wrote:

Hi folks

“Can of worms” is how this could be described!

 From various different sources (many thanks Paul, Mitch, Robbie) I have now 
managed to obtain (inter alia) lists of 31, 189, 863 and 916 modified amino 
acids - and there are other, longer (and possibly shorter and equimetric [is 
that even a word?] lists that I could create if I want to be more 
comprehensive! It’s certainly _possible_ that some of the members of an 
individual list are duplicates, but for my current purposes these should 
suffice nearly all the time (and for those cases where the list falls short, I 
would expect people to raise the issue directly with me…)

Once more, I knew this would be the place to ask!

Harry


On 24 Jun 2024, at 13:40, Robbie Joosten  wrote:

Hi Harry,

A BSc student in our lab just had a look at this. Here is the list of mappings 
pdb-redo uses: 
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
(second to last loop).

Cheers,
Robbie

pdb-redo-main/tools/pdb-redo-data.cif at trunk · PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to 
PDB-REDO/pdb-redo-main development by creating an account on GitHub.
github.com

From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] List of 3-letter codes of modified amino acids
  
Hi


An internet search doesn’t yield an obvious list of these (I did find a paper 
DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included 
appears to be dead - http://deposit.pdb.org/hetdictionary.txt).

I’m almost convinced that this has been asked here previously (if not 
recently), but a quick search through ccp4bb postings has not revealed it to me.

Can anyone help?

Harry


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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https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Harry Powell]

Hi folks

“Can of worms” is how this could be described!

From various different sources (many thanks Paul, Mitch, Robbie) I have now 
managed to obtain (inter alia) lists of 31, 189, 863 and 916 modified amino 
acids - and there are other, longer (and possibly shorter and equimetric [is 
that even a word?] lists that I could create if I want to be more 
comprehensive! It’s certainly _possible_ that some of the members of an 
individual list are duplicates, but for my current purposes these should 
suffice nearly all the time (and for those cases where the list falls short, I 
would expect people to raise the issue directly with me…)

Once more, I knew this would be the place to ask!

Harry

> On 24 Jun 2024, at 13:40, Robbie Joosten  wrote:
> 
> Hi Harry,
> 
> A BSc student in our lab just had a look at this. Here is the list of 
> mappings pdb-redo uses: 
> https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif 
> (second to last loop).
> 
> Cheers,
> Robbie
> 
> pdb-redo-main/tools/pdb-redo-data.cif at trunk · PDB-REDO/pdb-redo-main
> core pdb-redo script, tools and data files. Contribute to 
> PDB-REDO/pdb-redo-main development by creating an account on GitHub.
> github.com
> 
> From: CCP4 bulletin board  on behalf of Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk>
> Sent: Monday, June 24, 2024 2:03 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] List of 3-letter codes of modified amino acids
>  
> Hi
> 
> An internet search doesn’t yield an obvious list of these (I did find a paper 
> DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included 
> appears to be dead - http://deposit.pdb.org/hetdictionary.txt).
> 
> I’m almost convinced that this has been asked here previously (if not 
> recently), but a quick search through ccp4bb postings has not revealed it to 
> me.
> 
> Can anyone help?
> 
> Harry
> 
> 
> 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:
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Re: [ccp4bb] List of 3-letter codes of modified amino acids

[Robbie Joosten]

Hi Harry,

A BSc student in our lab just had a look at this. Here is the list of mappings 
pdb-redo uses: 
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif
 (second to last loop).

Cheers,
Robbie
[https://opengraph.githubassets.com/6fea661601fca9b8e8dbf2d994bd6f4fca81a6e4317848845d8ccb0349f0f171/PDB-REDO/pdb-redo-main]
pdb-redo-main/tools/pdb-redo-data.cif at trunk · 
PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to 
PDB-REDO/pdb-redo-main development by creating an account on GitHub.
github.com


From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] List of 3-letter codes of modified amino acids

Hi

An internet search doesn’t yield an obvious list of these (I did find a paper 
DOI:10.1016/j.jmgm.2006.08.004 that says there are 293, but the link included 
appears to be dead - http://deposit.pdb.org/hetdictionary.txt).

I’m almost convinced that this has been asked here previously (if not 
recently), but a quick search through ccp4bb postings has not revealed it to me.

Can anyone help?

Harry


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 
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Re: [ccp4bb] searching for ligands with double conformation

[Deborah Harrus]

Dear Anat,

Replying on behalf of Chris Thorpe:

The only reliable way I've found is to compare the conformations in each 
of the biological units and also to look for ALTLOCs. Obviously you can 
automate all of this, using BioPandas to compare peptide conformations 
(looking at position level RMSDs) and having some BioPython/Pymol code 
to deal with ALTLOCs and split them into different files.


Hope that helps!

Kind regards,

Deborah

On 24/06/2024 10:31, Anat Bashan wrote:


Dear CCP4 community,

I am interested in searching in the PDB for ligands that are in 
complex with proteins in the PDB that were deposited with a double 
conformation.


Does anyone know how to run such a search? How to define it?

Thanks a lot for your help,

Anat.

=
Anat Bashan , Ph.D Tel:972-8-9344289 
Senior staff scientist @The Ribosome Group

The Weizmann Institute of Science
The Department of Chemical and Structural Biology Mobile:972-52-3347229
Rehovot 7610001   e-mail: 
anat.bas...@weizmann.ac.il 


Israel

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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
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Cambridge CB10 1SD UK

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Re: [ccp4bb] Server to find structural similarity between nucleic acid structures

[Deborah Harrus]

Dear Marc,

I'm not sure if there are tools to find global similarity, but you can 
use tools like NASSAM (http://211.25.251.163/nassam/), WebFR3D 
(https://www.bgsu.edu/research/rna/web-applications/webfr3d.html) or 
RAG3D (http://www.biomath.nyu.edu/?q=RAG3D) to do substructure search.


Kind regards,

Deborah

On 24/06/2024 10:05, Marc Graille wrote:

Hello,

I am looking for a server that finds structural similarities between 
the structure of an RNA and all RNA structures present in the PDB, 
pretty much like DALI or PDB-eFold do for proteins.


Does anyone know if such server exists?
Thanks a loot for your help,

Best wishes,

Marc

—
*Marc GRAILLE, PhD*
DR1-CNRS

Head of the team: “Translation and degradation of eukaryotic mRNAs”

Laboratoire de Biologie Structurale de la Cellule  (BIOC); UMR7654; CNRS
*ÉCOLE POLYTECHNIQUE*
91128 PALAISEAU CEDEX
FRANCE
: +33 (0)1 69 33 48 90
https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes

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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

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Re: [ccp4bb] merging of datasets

[Kay Diederichs]

Dear Jordi,

for XDS/XSCALE users, there is XDSCC12 (see 
https://wiki.uni-konstanz.de/xds/index.php/Xdscc12 ).

It is integrated in XDSGUI (statistics tab) where it shows, for a single 
XDS_ASCII.HKL, how much batches of the run contribute towards CC1/2 of the 
dataset, i.e. what there delta-CC1/2 is. This e.g. allows to see where 
radiation damage sets in.

For use with merging of datasets, you create a XSCALE.INP with 

OUTPUT_FILE=WHATEVERNAME.HKL
INPUT_FILE=/some/where/first/XDS_ASCII.HKL
INPUT_FILE=/some/where/econd/XDS_ASCII.HKL
INPUT_FILE=/some/where/third/XDS_ASCII.HKL
... (as many INPUT_FILEs as you want)

Then you just run

xscale_par

and obtain XSCALE.LP and WHATEVERNAME.HKL (and a bunch of control files; if you 
are not interested in these, there are options that prevent their creation).

Finally, you run

xdscc12 WHATEVERNAME.HKL | tee XDSCC12.LP

and it will calculate the delta-CC1/2 statistics of each dataset, for each 
resolution shell.
It does this for the isomorphous signal (which is what you ask about), and for 
the anomalous signal (delta-CC1/2ano). 

There are options that modify the action and output of the program; you see 
them in the XDSwiki article or when you run with the -h option.

What should make its use easy is that XDSCC12 writes a file 
XSCALE.INP_rename_me that has the format of XSCALE.INP, but with the INPUT_FILE 
lines sorted by the quality of the datasets i.e. by their delta-CC1/2 . I'd 
read and edit XSCALE.INP_rename_me, remove the last one if it has a negative 
delta-CC1/2 , then rename to XSCALE.INP, and re-run xscale_par . If you have 
many datasets, this can be iterated; I hope you get the idea.

If you have questions, pls get back.

Hope this helps,
Kay





On Fri, 21 Jun 2024 15:15:34 +, Jordi Benach  wrote:

>Dear Everyone,
>Suppose you have three or more datasets and would like to choose the best 
>combination to merge and produce a higher quality dataset. I have been using 
>BLEND with mixed results. Additionally, BLEND doesn’t seem to accept datasets 
>with several runs (i.e., a dataset where several of its frames have been 
>removed, see next line).
>BLEND: “crystal_flag = 2:   crystal is rejected because data file is made up 
>of multiple runs”
>Apart from BLEND, what tools or methods do people use to achieve this? Using 
>CAD, SCALEIT, and/or POINTLESS should be helpful, but I haven’t found a 
>program that uses them to suggest the best dataset combination to merge.
>Thank you in advance for your help.
>Best regards,
>Jordi
>Jordi Benach, PhD
>LRL-CAT, Director & Head of Operations
>Sr. Director-Chemistry, DCRT
>Eli Lilly and Company
>Advanced Photon Source, Argonne National Laboratory, Building 438A
>9700 S. Cass Ave., Lemont, IL 60439 U.S.A.
>+1 630.252.0821 (office) | +1 630.209.4264 (mobile)
>benach_jo...@lilly.com | 
>www.lilly.com
>[cid:image001.png@01DAC3C3.F2C1B0F0]
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Re: [ccp4bb] merging of datasets

[Eleanor Dodson]

I second martin’s suggestion..

it is not essential but it is sensible to give the lively best as the first
entry then the other sets are scaled and indexed to match it..
I use ccp4i2 for this . You will get quite a voluminous report which is
very helpful

Good luck Eleanor


On Fri, 21 Jun 2024 at 17:26, Martin Malý  wrote:

> Dear Jordi,
>
> For this purpose, I would use AIMLESS (you can specify a list of unmerged
> data sets) or xia2.multiplex. Output log files should indicate which data
> sets or images to discard - then the merging can be re-run without them.
>
> Best regards,
> Martin
>
>
> On 21/06/2024 16:15, Jordi Benach wrote:
>
> Dear Everyone,
>
> Suppose you have three or more datasets and would like to choose the best
> combination to merge and produce a higher quality dataset. I have been
> using BLEND with mixed results. Additionally, BLEND doesn’t seem to accept
> datasets with several runs (i.e., a dataset where several of its frames
> have been removed, see next line).
>
> BLEND: “crystal_flag = 2:   crystal is rejected because data file is made
> up of multiple runs”
>
> Apart from BLEND, what tools or methods do people use to achieve this?
> Using CAD, SCALEIT, and/or POINTLESS should be helpful, but I haven’t found
> a program that uses *them* to suggest the best dataset combination to
> merge.
>
> Thank you in advance for your help.
>
> Best regards,
>
> Jordi
>
> *Jordi Benach, PhD*
> LRL-CAT, Director & Head of Operations
>
> Sr. Director-Chemistry, DCRT
> Eli Lilly and Company
>
> Advanced Photon Source, Argonne National Laboratory, Building 438A
>
> 9700 S. Cass Ave., Lemont, IL 60439 U.S.A.
> 
>
> +1 630.252.0821 (office) | +1 630.209.4264 (mobile)
>
> benach_jo...@lilly.com | www.lilly.com
>
> CONFIDENTIALITY NOTICE: This email message (including all attachments) is
> for the sole use of the intended recipient(s) and may contain confidential
> information. Any unauthorized review, use, disclosure, copying or
> distribution is strictly prohibited. If you are not the intended recipient,
> please contact the sender by reply email and destroy all copies of the
> original message.
>
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Re: [ccp4bb] merging of datasets

[Martin Malý]

Dear Jordi,

For this purpose, I would use AIMLESS (you can specify a list of 
unmerged data sets) or xia2.multiplex. Output log files should indicate 
which data sets or images to discard - then the merging can be re-run 
without them.


Best regards,
Martin

On 21/06/2024 16:15, Jordi Benach wrote:


Dear Everyone,

Suppose you have three or more datasets and would like to choose the 
best combination to merge and produce a higher quality dataset. I have 
been using BLEND with mixed results. Additionally, BLEND doesn’t seem 
to accept datasets with several runs (i.e., a dataset where several of 
its frames have been removed, see next line).


BLEND: “crystal_flag = 2:   crystal is rejected because data file is 
made up of multiple runs”


Apart from BLEND, what tools or methods do people use to achieve this? 
Using CAD, SCALEIT, and/or POINTLESS should be helpful, but I haven’t 
found a program that uses /them/ to suggest the best dataset 
combination to merge.


Thank you in advance for your help.

Best regards,

Jordi

*Jordi Benach, PhD*
LRL-CAT, Director & Head of Operations

Sr. Director-Chemistry, DCRT
Eli Lilly and Company

Advanced Photon Source, Argonne National Laboratory, Building 438A

9700 S. Cass Ave., Lemont, IL 60439 U.S.A.

+1 630.252.0821 (office) | +1 630.209.4264 (mobile)

benach_jo...@lilly.com | www.lilly.com 



CONFIDENTIALITY NOTICE: This email message (including all attachments) 
is for the sole use of the intended recipient(s) and may contain 
confidential information. Any unauthorized review, use, disclosure, 
copying or distribution is strictly prohibited. If you are not the 
intended recipient, please contact the sender by reply email and 
destroy all copies of the original message.





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Re: [ccp4bb] Extra density on Cysteine

[Mark J. van Raaij]

Dear Tina,

my guess would be minor oxidation of the cysteine. The green positive 
difference density suggests a bound atom in three different positions; this 
could however just be the first atom of something bigger like 
beta-mercaptoethanol, with the rest of that molecule too disordered to see. By 
eye-balling, the blue electron density does not look much bigger than expected 
for sulfur, so whatever it is, I would think it's very minor and probably not 
even worth modelling. 

I am also guessing this map is after refinement is almost complete and the 
overall difference map quite flat, so three sigmas of difference density (if 
that is what is contoured) may correspond to quite few electrons, i.e. low 
occupancy of the adduct.

Another explanation might be "anomalous behaviour" of the sulfur, similar to 
residual difference densities often observed near metal ions. A physicist will 
likely have a better idea about this than me.

Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


> On 21 Jun 2024, at 11:02, hsyu11gmail  wrote:
> 
> Dear all,
> 
> We recently solved a structure to 2.1 A, and found an additional Fo-Fc 
> density on the side chain of a cysteine residue. The structure has been 
> reported previously, and no modification found at this site. The distances 
> between the cysteine and other residues also does not appear to be long 
> enough for any modifications. 
> 
> Does anyone has an idea about this map?
> 
> Thanks.
> 
> Kind regards,
> Tina
> 
> 
> 
> 
> hsyu11gmail
> 
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Re: [ccp4bb] Off-topic: UCSF Chimera Download

[Kovtun, Oleksiy]

I realised i have its chimeraX, not the old chimera. Sorry.
O.

On 18. Jun 2024, at 18:21, Kovtun, Oleksiy 
mailto:oleksiy.kov...@mpinat.mpg.de>> wrote:

I dug out a MacOS dmg file, too. I will DM you a link.
O.



On 18. Jun 2024, at 18:09, Nicholas Clark 
mailto:ndcla...@buffalo.edu>> wrote:

Thanks for the responses. I’ve made multiple attempts over the last few days 
which is why I reached out. Maybe it’s just high traffic and I’ll have to keep 
trying.

Oleksiy, thanks for the offer but I’m on MacOS.

Best,

Nick


On Tue, Jun 18, 2024 at 12:07 PM Kovtun, Oleksiy 
mailto:oleksiy.kov...@mpinat.mpg.de>> wrote:
Hi Nick,

their web site goes offline from time to time. If you are on linux, I can share 
recent binaries.

Best,

Oleksiy


On 18. Jun 2024, at 17:53, Nicholas Clark 
>
 wrote:

I’m trying to navigate to the download page for UCSF Chimera but it does not 
seem to be working. Does anyone know of an alternative location?

Thanks,

Nick Clark




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Re: [ccp4bb] Off-topic: UCSF Chimera Download

[Kovtun, Oleksiy]

I dug out a MacOS dmg file, too. I will DM you a link.
O.



On 18. Jun 2024, at 18:09, Nicholas Clark 
mailto:ndcla...@buffalo.edu>> wrote:

Thanks for the responses. I’ve made multiple attempts over the last few days 
which is why I reached out. Maybe it’s just high traffic and I’ll have to keep 
trying.

Oleksiy, thanks for the offer but I’m on MacOS.

Best,

Nick


On Tue, Jun 18, 2024 at 12:07 PM Kovtun, Oleksiy 
mailto:oleksiy.kov...@mpinat.mpg.de>> wrote:
Hi Nick,

their web site goes offline from time to time. If you are on linux, I can share 
recent binaries.

Best,

Oleksiy


On 18. Jun 2024, at 17:53, Nicholas Clark 
>
 wrote:

I’m trying to navigate to the download page for UCSF Chimera but it does not 
seem to be working. Does anyone know of an alternative location?

Thanks,

Nick Clark




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Off-topic: UCSF Chimera Download

[Kovtun, Oleksiy]

Hi Nick,

their web site goes offline from time to time. If you are on linux, I can share 
recent binaries.

Best,

Oleksiy


On 18. Jun 2024, at 17:53, Nicholas Clark 
>
 wrote:

I’m trying to navigate to the download page for UCSF Chimera but it does not 
seem to be working. Does anyone know of an alternative location?

Thanks,

Nick Clark




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Off-topic: UCSF Chimera Download

[Andy Purkiss]

According to X, there is electrical work yesterday and today.

Downtime: The ChimeraX web site, web services (Blast Protein, Modeller tools, 
sequence realignment), mailing lists, and bug reporting will be down 9 AM 
Pacific time Monday June 17 to 5 PM Tuesday June 18 for building electrical 
upgrades.

Hope this helps.

Andy


From: CCP4 bulletin board  on behalf of Nicholas Clark 
<b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk>
Sent: 18 June 2024 17:09
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Off-topic: UCSF Chimera Download


External Sender: Use caution.

Thanks for the responses. I’ve made multiple attempts over the last few days 
which is why I reached out. Maybe it’s just high traffic and I’ll have to keep 
trying.

Oleksiy, thanks for the offer but I’m on MacOS.

Best,

Nick


On Tue, Jun 18, 2024 at 12:07 PM Kovtun, Oleksiy 
mailto:oleksiy.kov...@mpinat.mpg.de>> wrote:
Hi Nick,

their web site goes offline from time to time. If you are on linux, I can share 
recent binaries.

Best,

Oleksiy


On 18. Jun 2024, at 17:53, Nicholas Clark 
<b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk<mailto:b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk>>
 wrote:

I’m trying to navigate to the download page for UCSF Chimera but it does not 
seem to be working. Does anyone know of an alternative location?

Thanks,

Nick Clark




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Re: [ccp4bb] Off-topic: UCSF Chimera Download

[Nicholas Clark]

Thanks for the responses. I’ve made multiple attempts over the last few
days which is why I reached out. Maybe it’s just high traffic and I’ll have
to keep trying.

Oleksiy, thanks for the offer but I’m on MacOS.

Best,

Nick


On Tue, Jun 18, 2024 at 12:07 PM Kovtun, Oleksiy <
oleksiy.kov...@mpinat.mpg.de> wrote:

> Hi Nick,
>
> their web site goes offline from time to time. If you are on linux, I can
> share recent binaries.
>
> Best,
>
> Oleksiy
>
>
> On 18. Jun 2024, at 17:53, Nicholas Clark <
> b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> I’m trying to navigate to the download page for UCSF Chimera but it does
> not seem to be working. Does anyone know of an alternative location?
>
> Thanks,
>
> Nick Clark
>
>
> --
>
> 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] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Wladek Minor]

James,

This is correct. To my knowledge, the only  result of BD2K initiative 
which is still alive (barely) is proteindiffraction.org.  I know that 
PDBj is planning to pick-up the data but they do not have funds to keep 
the entire system alive, i.e. check of netadata, processing, doi 
handlig, etc.


Best regards

Wladek

On 6/14/2024 10:52 PM, James Holton wrote:
I seem to recall Wladek mentioning that he has been trying to keep 
proteindiffraction.org alive using his own personal funds, which must 
be difficult.  The NIH grant for Proteindiffraction.org was U01 
HG008424, which had a Project End date of 2018-05-31, and no record of 
a renewal. It was part of the NIH BD2K (Big Data to Knowledge) 
program, but the website for BD2K appears to be a broken link now. The 
final archive.org of it lists an NIH Request for Information 
NOT-OD-16-091 in 2016, where the community was solicited to fill out a 
survey about how useful the program was.  Did anyone here fill out 
that survey?


-James Holton
MAD Scientist

On 6/13/2024 12:24 PM, John R Helliwell wrote:

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago,
there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its excellent work were presented at IUCr 
Melbourne.
Greetings,
John

Emeritus Professor John R Helliwell DSc





On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
Dear John,

 Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

 Best wishes,

Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:

Dear Martin,Thankyou.Unfortunately I have no explanation to offer onhttps://proteindiffraction.org/;>proteindiffraction.org 
currently.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin 
Malý martin.maly...@email.cz wrote:





Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/;>https://proteindiffraction.org/ (IRRMC) was rescued. I
preferred this website but they stopped receiving new data sets - or
at least they do not reply to my emails for more than a year. I am
worried that the website will disappear and also all the uploaded
data sets will be gone...
Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell
  wrote:


  Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published 
this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html;>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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--
Dr. Wladek Minor
Harrison Distinguished Professor
Department of Molecular Physiology and Biological Physics
Phone: 434-243-6865
Fax: 434-243-2981
https://minorlab.org


US-mail address:
Department of Molecular Physiology and Biological Physics
University of Virginia
PO Box 800736, Charlottesville, VA 22908-0736

Fed-Ex address:
Department of Molecular Physiology and Biological Physics
1340 Jefferson Park Avenue
University of Virginia
Charlottesville, VA 22908






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This message was issued 

Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Wladek Minor]

Dear Martin,

I am the one who presented in Melbourne. When you contact support, 
please send cc to wla...@minorlab.org. Just for your information, 
proteindiffraction.org is not supported by NIH since 2018.


Best regards

Wladek


On 6/14/2024 1:55 PM, Martin Malý wrote:

Dear John,
Please could you give us an advice who to contact - who presented in 
Melbourne?
I think there are more of us who are not successful in contacting 
their support.

Thank you.
Martin

On 13/06/2024 20:24, John R Helliwell wrote:

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a 
month ago,

there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its excellent work were presented at 
IUCr Melbourne.

Greetings,
John

Emeritus Professor John R Helliwell DSc




On 13 Jun 2024, at 19:27, Gerard Bricogne  
wrote:

Dear John,

 Is this not a matter on which internal communication within the 
IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be 
expected to

be able to throw some light?

 Best wishes,

    Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:
Dear 
Martin,Thankyou.Unfortunately I have no explanation 
to offer onhref="https://proteindiffraction.org/;>proteindiffraction.org 
currently.Greetings,Johndir="ltr">Emeritus Professor John R Helliwell 
DScdir="ltr">On 13 Jun 2024, at 10:41, 
Martin Malý martin.maly...@email.cz 
wrote:dir="ltr">



    



    Dear John,
    Thank you for the link. It would be great if
    href="https://proteindiffraction.org/;>https://proteindiffraction.org/ 
(IRRMC) was rescued. I
    preferred this website but they stopped receiving new data sets 
- or

    at least they do not reply to my emails for more than a year. I am
    worried that the website will disappear and also all the uploaded
    data sets will be gone...
    Cheers,
    Martin
    
    On 12/06/2024 20:44, John R Helliwell
  wrote:
    
    cite="mid:025c572c-c078-40d5-9fca-e697aba6b...@gmail.com">

  Dear Colleagues,
Our article on this topic, which I imagine will be of keen 
interest, published this afternoon, is available open access from 
this weblink:-
href="https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html;>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html

Best wishes,
John
Emeritus Professor John R Helliwell DSc

 



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--
Dr. Wladek Minor
Harrison Distinguished Professor
Department of Molecular Physiology and Biological Physics
Phone: 434-243-6865
Fax: 434-243-2981
https://minorlab.org


US-mail address:
Department of Molecular Physiology and Biological Physics
University of Virginia
PO Box 800736, Charlottesville, VA 22908-0736

Fed-Ex address:
Department of Molecular Physiology and Biological Physics
1340 Jefferson Park Avenue
University of Virginia
Charlottesville, VA 22908






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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Jon Cooper]

Comparing maps sounds just like the sort of thing the Uppsala suite did. Maybe 
you can find an old binary for mapman or mapman2(?) or compile it from Martin 
Winn's github page. The closest I can find is EDSTATS which I think is in the 
old ccp4 gui.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 14/06/2024 20:58, Matt Mcleod  wrote:

> I should clarify. I am mostly concerned about the electron density map.
>
> I want to make sure that I can most closely compare the maps from two 
> different quality structures, rather than the datasets themselves via CC1/2 
> or other metrics. This is more so for interpreting structural changes.
>
> For example, if there is sparse density for some particular thing indicating 
> partial occupancy, how can I compare those two maps. So for low-resolution 
> datasets, maybe there is less density but is that because of data quality or 
> because in that dataset there is a lower occupancy through some meaningful 
> structural change (compared to higher resolution/better data)?
>
> On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am wondering what the best practice is to compare datasets that are of the 
>> same protein but different quality, for instance 2 vs. 3 A.
>>
>> I know that truncating the structures to the same resolution bin is alright, 
>> but the data quality in the lower resolution bins are also not the same. Is 
>> there a way to "inject" noise into the data such that the bins are more 
>> similar?
>>
>> These datasets cannot be recollected at higher resolution since they are 
>> collected at increasingly high pressure, and the resolution change is 
>> anticorrelated with the pressure; no way to get around crystal stability.
>>
>> Any suggestions are appreciated,
>> Matt
>>
>> 
>>
>> 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/
>
> --
>
> Matthew Jordan McLeod, PhD
> Post-Doctoral Fellow - Cornell University
>
> ---
>
> 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] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[John R Helliwell]

Hello James,I have checked the IUCr Public Forum Diffraction Data Deposition Working Group postings and there is no posting about an ROI for the IRRMC. I don’t recall mention of it being made on this bb either, but my memory may be wrong.Answering ROIs are important, as you are correctly stressing for the current MSR beamlines ROI. A famous lesson this side of the pond is that the majority of young people, overwhelmingly in favour of Remain in the EU, didn’t vote in the Brexit referendum in 2016. The outcome of that lack of participation in the vote was the disaster that is Brexit, bad for UK and bad for the EU. Greetings,John Emeritus Professor John R Helliwell DScOn 15 Jun 2024, at 03:52, James Holton  wrote:

  

  
  
I seem to recall Wladek mentioning that he has been trying to keep
proteindiffraction.org alive using his own personal funds, which
must be difficult.  The NIH grant for Proteindiffraction.org was U01 HG008424, which had a
  Project End date of 2018-05-31, and no record of a
renewal. It was part of the NIH BD2K (Big Data to Knowledge)
program, but the website for BD2K appears to be a broken link now.
The
final archive.org of it lists an NIH Request for Information NOT-OD-16-091 in 2016, where the community was
  solicited to fill out a survey about how useful the program was. 
  Did anyone here fill out that survey? 
  
  -James Holton
  MAD Scientist

On 6/13/2024 12:24 PM, John R Helliwell
  wrote:


  Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago, 
there is currently no news of proteindiffraction.org to share. 
Certainly detailed reports of its excellent work were presented at IUCr Melbourne. 
Greetings,
John 

Emeritus Professor John R Helliwell DSc





  
On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
Dear John,

Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

Best wishes,

   Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:


  Dear Martin,Thankyou.Unfortunately I have no explanation to offer on"https://proteindiffraction.org/">proteindiffraction.org currently.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin Malý martin.maly...@email.cz wrote:


   


   Dear John,
   Thank you for the link. It would be great if
   "https://proteindiffraction.org/">https://proteindiffraction.org/ (IRRMC) was rescued. I
   preferred this website but they stopped receiving new data sets - or
   at least they do not reply to my emails for more than a year. I am
   worried that the website will disappear and also all the uploaded
   data sets will be gone...
   Cheers,
   Martin
   
   On 12/06/2024 20:44, John R Helliwell
 wrote:
   
   "mid:025c572c-c078-40d5-9fca-e697aba6b...@gmail.com">
 Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:-
"https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html">https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[James Holton]

I seem to recall Wladek mentioning that he has been trying to keep 
proteindiffraction.org alive using his own personal funds, which must be 
difficult.  The NIH grant for Proteindiffraction.org was U01 HG008424, 
which had a Project End date of 2018-05-31, and no record of a renewal. 
It was part of the NIH BD2K (Big Data to Knowledge) program, but the 
website for BD2K appears to be a broken link now. The final archive.org 
of it lists an NIH Request for Information NOT-OD-16-091 in 2016, where 
the community was solicited to fill out a survey about how useful the 
program was. Did anyone here fill out that survey?


-James Holton
MAD Scientist

On 6/13/2024 12:24 PM, John R Helliwell wrote:

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago,
there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its excellent work were presented at IUCr 
Melbourne.
Greetings,
John

Emeritus Professor John R Helliwell DSc





On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
Dear John,

 Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

 Best wishes,

Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:

Dear Martin,Thankyou.Unfortunately I have no explanation to offer onhttps://proteindiffraction.org/;>proteindiffraction.org 
currently.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin 
Malý martin.maly...@email.cz wrote:





Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/;>https://proteindiffraction.org/ (IRRMC) was rescued. I
preferred this website but they stopped receiving new data sets - or
at least they do not reply to my emails for more than a year. I am
worried that the website will disappear and also all the uploaded
data sets will be gone...
Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell
  wrote:


  Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published 
this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html;>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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Re: [ccp4bb] Comparing datasets with different resolution/quality

[Kay Diederichs]

Hi Matt,

I guess that the datasets have the same spacegroup and very similar cell 
parameters?

And that you have two similar models that you obtained by refining against the 
datasets?

What you can do is to find out which dataset gives the better model, and is 
therefore better 
(i.e. generally more useful - but maybe not in every place of the e.d. map).
To arrive at this conclusion, use the two models for a paired-refinement-type 
of comparison, i.e.

a) note Rwork_AA,Rfree_AA of model A (obtained by refinement against dataset A)
b) note Rwork_BB,Rfree_BB of model B (obtained by refinement against dataset B)
c) rigid-body-and-overall-B refine model A against dataset B to obtain 
Rwork_AB,Rfree_AB
d) rigid-body-and-overall-B refine model B against dataset A to obtain 
Rwork_BA,Rfree_BA
e) if Rfree_AB < Rfree_BB then dataset A is better than dataset B (and 
conversely)
f) check the result of e): if Rfree_BA > Rfree_AA (and conversely) then this 
confirms the result from e)

Hope that this at least is a step towards the insights you're after!

Best, Kay

On Fri, 14 Jun 2024 15:58:41 -0400, Matt Mcleod  wrote:

>I should clarify.  I am mostly concerned about the electron density map.
>
>I want to make sure that I can most closely compare the maps from two
>different quality structures, rather than the datasets themselves via CC1/2
>or other metrics.  This is more so for interpreting structural changes.
>
>For example, if there is sparse density for some particular thing
>indicating partial occupancy, how can I compare those two maps.  So for
>low-resolution datasets, maybe there is less density but is that because of
>data quality or because in that dataset there is a lower occupancy through
>some meaningful structural change (compared to higher resolution/better
>data)?
>
>On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:
>
>> Hi all,
>>
>> I am wondering what the best practice is to compare datasets that are of
>> the same protein but different quality, for instance 2 vs. 3 A.
>>
>> I know that truncating the structures to the same resolution bin is
>> alright, but the data quality in the lower resolution bins are also not the
>> same.  Is there a way to "inject" noise into the data such that the bins
>> are more similar?
>>
>> These datasets cannot be recollected at higher resolution since they are
>> collected at increasingly high pressure, and the resolution change is
>> anticorrelated with the pressure; no way to get around crystal stability.
>>
>> Any suggestions are appreciated,
>> Matt
>>
>> 
>>
>> 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/
>>
>
>
>--
>*Matthew Jordan McLeod, PhD*
>*Post-Doctoral Fellow - Cornell University*
>
>
>
>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] Comparing datasets with different resolution/quality

[Matt Mcleod]

I should clarify.  I am mostly concerned about the electron density map.

I want to make sure that I can most closely compare the maps from two
different quality structures, rather than the datasets themselves via CC1/2
or other metrics.  This is more so for interpreting structural changes.

For example, if there is sparse density for some particular thing
indicating partial occupancy, how can I compare those two maps.  So for
low-resolution datasets, maybe there is less density but is that because of
data quality or because in that dataset there is a lower occupancy through
some meaningful structural change (compared to higher resolution/better
data)?

On Fri, 14 Jun 2024 at 14:16, Matt McLeod  wrote:

> Hi all,
>
> I am wondering what the best practice is to compare datasets that are of
> the same protein but different quality, for instance 2 vs. 3 A.
>
> I know that truncating the structures to the same resolution bin is
> alright, but the data quality in the lower resolution bins are also not the
> same.  Is there a way to "inject" noise into the data such that the bins
> are more similar?
>
> These datasets cannot be recollected at higher resolution since they are
> collected at increasingly high pressure, and the resolution change is
> anticorrelated with the pressure; no way to get around crystal stability.
>
> Any suggestions are appreciated,
> Matt
>
> 
>
> 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/
>


-- 
*Matthew Jordan McLeod, PhD*
*Post-Doctoral Fellow - Cornell University*



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Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

[Jeffrey B Bonanno]

Correction made below - AMV in my original message should read AMX of course
__

BNL NSLS-II, FMX or AMX beamlines: overall coordinator Vivian Stojanoff

Beamline scientists
FMX Wuxian Shi or Martin Fuchs or Alexei Soares

AMX Jean Jakoncic or Edwin Lazo or Dale Kreitler

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Friday, June 14, 2024 2:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the "Phish Alert" button on the top right of the 
Outlook dashboard to report any suspicious emails.

OK, folks, the last day to voice your opinion on this is Monday June 17.

survey is here:  https://www.research.net/r/P30_RFI

I encourage anyone who has used these synchrotrons to chime in. Your opinion 
matters, but the NIH cannot read your mind!  I personally think it very 
important that they get an accurate picture.

Some of you might not be sure if the beamline you usually use is one of these 
"MSR" things? Well, if you read CCP4BB and have used or plan to use the ALS, 
SSRL, CHESS, NSLS-II, or the APS beamlines GM/CA CAT, BioCAT or NE-CAT to 
collect X-ray diffraction, SAXS, XCT or, XFP data then you are one of the 
people the NIH wants to hear from.

Another way to know if you have used these resources is if any of these names 
ring a bell.  Was the person who scheduled your beam time Jane Tanamachi? Stacy 
Ortega? or Kathryn Burnett?  Then you used the ALS-ENABLE MSR.  If the beamline 
scientist who supported you was one of
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg Hura, 
Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony Rosalez, Daniil 
Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros, then you used an 
MSR-supported beamline.

If your beam time person was Lisa Dunn, you used the SSRL MSR. The SSRL 
beamline scientists who may have supported you are: Clyde Smith, Silvia Russi, 
Irimpan Mathews, Tzanko Doukov, Ailiena Maggiolo, Darya Marchany-Rivera, and 
Aina Cohen.

These are just to name two MSRs that I am personally familiar with. Let me know 
who I forgot.

Details on all the MSR grants are here:
https://www.nigms.nih.gov/grants/Pages/Mature-Synchrotron-Resources.aspx

Have a nice weekend everyone, and I encourage you to take a moment to 
participate. The survey is anonymous and although it would be nice of you to 
answer all 15 questions, all responses are optional. Better to have your voice 
heard that not at all.

-James Holton
MAD Scientist

On 5/20/2024 5:32 PM, Paul Adams wrote:
> Dear Colleagues,
>
> Apologies for the US-centric posting, but I think this is of interest to many 
> of the bulletin board subscribers who make use of synchrotron facilities in 
> the US.
>
> NIH is seeking feedback on the Mature Synchrotron Program:
>
>
> https://gran/
> ts.nih.gov%2Fgrants%2Fguide%2Fnotice-files%2FNOT-GM-24-019.html=0
> 5%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7C44c31427b6784c0dc53708dc8
> c9dd92b%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C63853985691876247
> 3%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6
> Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=uBzcefsreyYJPHwhuJmVxAYrZj0A
> Q6NPEsjtNcqmKpo%3D=0
>
> This program supports synchrotron-based user resources where the technologies 
> are at an advanced level, including Macromolecular Crystallography, 
> Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other 
> synchrotron-based techniques that generate important data, with an emphasis 
> on structural biology.
>
> Responses to the RFI will be accepted through 6/17/2024. All comments
> will be anonymous and should be submitted electronically via a web
> form at:
> https://www/.
> research.net%2Fr%2FP30_RFI=05%7C02%7Cjeffrey.bonanno%40einsteinme
> d.edu%7C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c089a82dfd51e
> 62025%7C0%7C0%7C638539856918767402%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
> wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C
> data=%2Begdvk1GWC4laLwqyYGHyzKlgp%2Fb6xJfHCAKpwRORVQ%3D=0
>
> As the Director of one of the resources it has been suggested that I help 
> make the community aware of the RFI, so there is the opportunity to provide 
> feedback in a timely manner. Feel free to pass this on to any of your 
> colleagues who may be interested.
>
>Cheers,
>   Paul
>
> --
> Paul Adams (he/him/his)
> Associate Laboratory Director for Biosciences, LBL (https://bio/
> sciences.lbl.gov%2F=05%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7
> C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c0

Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

[Jeffrey B Bonanno]

BNL NSLS-II, FMX or AMX beamlines: overall coordinator Vivian Stojanoff

Beamline scientists
FMX Wuxian Shi or Martin Fuchs or Alexei Soares
AMV Jean Jakoncic or Edwin Lazo or Dale Kreitler

Jeffrey B. Bonanno, Ph.D.
Department of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Avenue
Bronx, NY 10461
off. 718-430-2452 fax. 718-430-8565
email jeffrey.bona...@einsteinmed.org

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Friday, June 14, 2024 2:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the "Phish Alert" button on the top right of the 
Outlook dashboard to report any suspicious emails.

OK, folks, the last day to voice your opinion on this is Monday June 17.

survey is here:  https://www.research.net/r/P30_RFI

I encourage anyone who has used these synchrotrons to chime in. Your opinion 
matters, but the NIH cannot read your mind!  I personally think it very 
important that they get an accurate picture.

Some of you might not be sure if the beamline you usually use is one of these 
"MSR" things? Well, if you read CCP4BB and have used or plan to use the ALS, 
SSRL, CHESS, NSLS-II, or the APS beamlines GM/CA CAT, BioCAT or NE-CAT to 
collect X-ray diffraction, SAXS, XCT or, XFP data then you are one of the 
people the NIH wants to hear from.

Another way to know if you have used these resources is if any of these names 
ring a bell.  Was the person who scheduled your beam time Jane Tanamachi? Stacy 
Ortega? or Kathryn Burnett?  Then you used the ALS-ENABLE MSR.  If the beamline 
scientist who supported you was one of
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg Hura, 
Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony Rosalez, Daniil 
Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros, then you used an 
MSR-supported beamline.

If your beam time person was Lisa Dunn, you used the SSRL MSR. The SSRL 
beamline scientists who may have supported you are: Clyde Smith, Silvia Russi, 
Irimpan Mathews, Tzanko Doukov, Ailiena Maggiolo, Darya Marchany-Rivera, and 
Aina Cohen.

These are just to name two MSRs that I am personally familiar with. Let me know 
who I forgot.

Details on all the MSR grants are here:
https://www.nigms.nih.gov/grants/Pages/Mature-Synchrotron-Resources.aspx

Have a nice weekend everyone, and I encourage you to take a moment to 
participate. The survey is anonymous and although it would be nice of you to 
answer all 15 questions, all responses are optional. Better to have your voice 
heard that not at all.

-James Holton
MAD Scientist

On 5/20/2024 5:32 PM, Paul Adams wrote:
> Dear Colleagues,
>
> Apologies for the US-centric posting, but I think this is of interest to many 
> of the bulletin board subscribers who make use of synchrotron facilities in 
> the US.
>
> NIH is seeking feedback on the Mature Synchrotron Program:
>
>
> https://gran/
> ts.nih.gov%2Fgrants%2Fguide%2Fnotice-files%2FNOT-GM-24-019.html=0
> 5%7C02%7Cjeffrey.bonanno%40einsteinmed.edu%7C44c31427b6784c0dc53708dc8
> c9dd92b%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C63853985691876247
> 3%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6
> Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=uBzcefsreyYJPHwhuJmVxAYrZj0A
> Q6NPEsjtNcqmKpo%3D=0
>
> This program supports synchrotron-based user resources where the technologies 
> are at an advanced level, including Macromolecular Crystallography, 
> Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other 
> synchrotron-based techniques that generate important data, with an emphasis 
> on structural biology.
>
> Responses to the RFI will be accepted through 6/17/2024. All comments
> will be anonymous and should be submitted electronically via a web
> form at:
> https://www/.
> research.net%2Fr%2FP30_RFI=05%7C02%7Cjeffrey.bonanno%40einsteinme
> d.edu%7C44c31427b6784c0dc53708dc8c9dd92b%7C9c01f0fd65e040c089a82dfd51e
> 62025%7C0%7C0%7C638539856918767402%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4
> wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C
> data=%2Begdvk1GWC4laLwqyYGHyzKlgp%2Fb6xJfHCAKpwRORVQ%3D=0
>
> As the Director of one of the resources it has been suggested that I help 
> make the community aware of the RFI, so there is the opportunity to provide 
> feedback in a timely manner. Feel free to pass this on to any of your 
> colleagues who may be interested.
>
>Cheers,
>   Paul
>
> --
> Paul Adams (he/him/his)
> Associate Laboratory Director for Biosciences, LBL
> (https://bio/
> sciences.lbl.gov%2F=05%7C02%7Cjeffrey.bonanno%40einst

Re: [ccp4bb] NIGMS Mature Synchrotron Program Evaluation

[James Holton]

OK, folks, the last day to voice your opinion on this is Monday June 17.

survey is here:  https://www.research.net/r/P30_RFI

I encourage anyone who has used these synchrotrons to chime in. Your 
opinion matters, but the NIH cannot read your mind!  I personally think 
it very important that they get an accurate picture.


Some of you might not be sure if the beamline you usually use is one of 
these "MSR" things? Well, if you read CCP4BB and have used or plan to 
use the ALS, SSRL, CHESS, NSLS-II, or the APS beamlines GM/CA CAT, 
BioCAT or NE-CAT to collect X-ray diffraction, SAXS, XCT or, XFP data 
then you are one of the people the NIH wants to hear from.


Another way to know if you have used these resources is if any of these 
names ring a bell.  Was the person who scheduled your beam time Jane 
Tanamachi? Stacy Ortega? or Kathryn Burnett?  Then you used the 
ALS-ENABLE MSR.  If the beamline scientist who supported you was one of 
these: James Holton, George Meigs, Banu Sankaran, Scott Classen, Greg 
Hura, Michael Hammel, Jay Nix, Kevin Royal, Jeff Dickert, Anthony 
Rosalez, Daniil Prighozin, Corie Ralston, Marc Allaire, or Mark LeGros, 
then you used an MSR-supported beamline.


If your beam time person was Lisa Dunn, you used the SSRL MSR. The SSRL 
beamline scientists who may have supported you are: Clyde Smith, Silvia 
Russi, Irimpan Mathews, Tzanko Doukov, Ailiena Maggiolo, Darya 
Marchany-Rivera, and Aina Cohen.


These are just to name two MSRs that I am personally familiar with. Let 
me know who I forgot.


Details on all the MSR grants are here:
https://www.nigms.nih.gov/grants/Pages/Mature-Synchrotron-Resources.aspx

Have a nice weekend everyone, and I encourage you to take a moment to 
participate. The survey is anonymous and although it would be nice of 
you to answer all 15 questions, all responses are optional. Better to 
have your voice heard that not at all.


-James Holton
MAD Scientist

On 5/20/2024 5:32 PM, Paul Adams wrote:

Dear Colleagues,

Apologies for the US-centric posting, but I think this is of interest to many 
of the bulletin board subscribers who make use of synchrotron facilities in the 
US.

NIH is seeking feedback on the Mature Synchrotron Program:

https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html

This program supports synchrotron-based user resources where the technologies 
are at an advanced level, including Macromolecular Crystallography, Small-Angle 
and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based 
techniques that generate important data, with an emphasis on structural biology.

Responses to the RFI will be accepted through 6/17/2024. All comments will be 
anonymous and should be submitted electronically via a web form at: 
https://www.research.net/r/P30_RFI

As the Director of one of the resources it has been suggested that I help make 
the community aware of the RFI, so there is the opportunity to provide feedback 
in a timely manner. Feel free to pass this on to any of your colleagues who may 
be interested.

   Cheers,
Paul

--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov)
Principal Investigator, Computational Crystallography Initiative, LBL 
(http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute 
(http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source 
(http://als-enable.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, UC Berkeley 
(http://bioeng.berkeley.edu)
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley 
(http://compbiochem.berkeley.edu)

Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul
ORCID: -0001-9333-8219

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.

Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ]
--



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Re: [ccp4bb] help with wwPDB validation warning

[Edward Berry]

This old message claims that / =  "weighted" by s.

If counting error is significant, s will be larger for stronger reflections, which are likely to 
have small I/s,  so in general /  > unweighted . As Werten points 
out.

However this seems to be the opposite of the OP's situation, if both measures 
refer to the same outer shell.
EAB
---



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--- Begin Message ---



b...@freesurf.fr wrote:

***  For details on how to be removed from this list visit the  ***
***  CCP4 home page http://www.ccp4.ac.uk ***




From these we calculate a weighted mean  and an error estimate of

the mean sd(), and a ratio for that unique reflection
/sd()

What is printed as Mn(I)/sd is the mean value of that ratio for all
reflections (possibly in a resolution bin) ie





Which is very different (!) from anything one could extract from a
Scalepack/HKL2000 output file, which only lists average intensity and
average sigma (in the final table at the end). The ratio of those two
numbers, i.e. /, tends to be considerably more "optimistic" than
a proper .



Werten leaves it as an exercise for the reader
to verify this. Here is my submission:

The (ratio of means) is equivalent to a weighted
(mean of ratios):

/  = sum(I)/n / sum(s)/n

 = sum (I)  / sum(s)

 = sum(s*(I/s)) / sum(s)

 =  "weighted" by s

This means /  looks like  but with more
weight given to those measurements with large s.
If the standard deviation is related to counting
error, then s is larger for strong reflections
(yes of course as a percentage it is smaller
for strong reflections, but in absolute value
it is larger).
Thus the statistic / is weighted toward
strong reflections, and will be more optimistic
than unweighted .

The next-to-last table of truncate output lists
, /, , / vs resolution.
In the critical last shells  and /
tend to be the same, perhaps because all
reflections are around the noise level and s
is dominated by background counts so that all
reflections are weighted equally.


for R-type factors (error/magnitude) the ratio of
the means (as in R-merge) is more optimistic
than the mean of the ratios (as in std deviation),
and by a much larger extent: weighted by I,
whereas "s" varies at most as the sqrt(I).
If we used the mean ratio the result would be
to horrible to contemplate, with all those weak
reflections at the noise level weighted equally
with the strong! But seriously, it makes some
sense for a statistic to be weighted toward the
strong reflections, since they contribute more
to the map. Who cares if a reflection measurement
has 70% error if it is so weak that it could be
omitted completely with no visible effect on
the map?

Ed


Best regards,

   S. Werten










--- End Message ---

Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[John R Helliwell]

Dear MartinHere is the weblink to our IUCr 2023 Committee on Data Workshop in Melbourne:-(IUCr) Melbourne Workshopiucr.orgPresentations are available for our speakers as you will see theirin . The IRRMC talk was given by Wladek Minor. I hope you can join us at IUCr 2026 Calgary as we progress this important theme which I am pleased to see you are enthusiastic about. Raw diffraction data archiving offers us great opportunities as a science.Greetings,John Emeritus Professor John R Helliwell DScOn 14 Jun 2024, at 17:56, Martin Malý  wrote:Dear John,Please could you give us an advice who to contact - who presented in Melbourne?I think there are more of us who are not successful in contacting their support.Thank you.MartinOn 13/06/2024 20:24, John R Helliwell wrote:Dear Gerard,Quite so. But, as this CCP4bb has also observed in emails about a month ago,there is currently no news of proteindiffraction.org to share.Certainly detailed reports of its excellent work were presented at IUCr Melbourne.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:Dear John, Is this not a matter on which internal communication within the IUCr'sCommDat (https://www.iucr.org/resources/data/commdat) would be expected tobe able to throw some light? Best wishes,    Gerard--On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:Dear Martin,Thankyou.Unfortunately I have no explanation to offer onproteindiffraction.org currently.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin Malý martin.maly...@email.cz wrote:        Dear John,    Thank you for the link. It would be great if    https://proteindiffraction.org/ (IRRMC) was rescued. I    preferred this website but they stopped receiving new data sets - or    at least they do not reply to my emails for more than a year. I am    worried that the website will disappear and also all the uploaded    data sets will be gone...    Cheers,    Martin        On 12/06/2024 20:44, John R Helliwell  wrote:          Dear Colleagues,Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:-https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.htmlBest wishes,JohnEmeritus Professor John R Helliwell DScTo unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BBA=1This 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=1To unsubscribe from the CCP4BB list, click the following link:https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1This 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/

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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Martin Malý]

Dear John,
Please could you give us an advice who to contact - who presented in 
Melbourne?
I think there are more of us who are not successful in contacting their 
support.

Thank you.
Martin

On 13/06/2024 20:24, John R Helliwell wrote:

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago,
there is currently no news of proteindiffraction.org to share.
Certainly detailed reports of its excellent work were presented at IUCr 
Melbourne.
Greetings,
John

Emeritus Professor John R Helliwell DSc





On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
Dear John,

 Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

 Best wishes,

Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:

Dear Martin,Thankyou.Unfortunately I have no explanation to offer onhttps://proteindiffraction.org/;>proteindiffraction.org 
currently.Greetings,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin 
Malý martin.maly...@email.cz wrote:





Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/;>https://proteindiffraction.org/ (IRRMC) was rescued. I
preferred this website but they stopped receiving new data sets - or
at least they do not reply to my emails for more than a year. I am
worried that the website will disappear and also all the uploaded
data sets will be gone...
Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell
  wrote:


  Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published 
this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html;>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Clemens Vonrhein]

Dear Martin,

On Thu, Jun 13, 2024 at 10:40:43AM +0100, Martin Malý wrote:
> Thank you for the link. It would be great if https://proteindiffraction.org/
> (IRRMC) was rescued.

They are back in business since a couple of months now - at least
regarding new data appearing there.

> I preferred this website but they stopped receiving new data sets -
> or at least they do not reply to my emails for more than a year.

That's true: no luck with that for me either since last
summer. Unfortunately the website has no information (that I can find)
who to contact for support or questions - so maybe my emails just went
to the wrong addresses.

> I am worried that the website will disappear and also all the uploaded data
> sets will be gone...

Very, very possible (same happened with e.g. the original JCSG
repository with all the originally processed data and a huge amount of
meta-data gone now [1]). In that respect a site like Zeonodo.org
(backed by big players like EC, OpenAIRE, CERN etc) is much more
likely to stay up - or at least have a plan for when something new
replaces it.

Of course, something generic like Zenodo is not dealing just with MX
data and therefore doesn't provide some intrinsic template to show
more than just file downloads. But since (1) all our detectors,
beamlines and inhouse instruments now write perfect, complete and rich
meta-data into the associated image headers (or HDF5 containers), and
(2) we all deposit meta-data rich models and multi-dataset reflection
data with correct information into the PDB, this is much less
important nowadays ... right?  ;-)

Cheers

Clemens

[1] The wayback machine at archive.org comes to rescue here
... sometimes.



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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Gerard Bricogne]

Dear John,

 Is this not a matter on which internal communication within the IUCr's
CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
be able to throw some light?

 Best wishes,

Gerard

--
On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:
> Dear 
> Martin,Thankyou.Unfortunately I have no explanation to offer 
> on href="https://proteindiffraction.org/;>proteindiffraction.org 
> currently.Greetings,John dir="ltr">Emeritus Professor John R Helliwell 
> DSc dir="ltr">On 13 Jun 2024, at 10:41, Martin Malý 
> martin.maly...@email.cz wrote: type="cite">
> 
>   
> 
>   
>   
> Dear John,
> Thank you for the link. It would be great if
>  href="https://proteindiffraction.org/;>https://proteindiffraction.org/ 
> (IRRMC) was rescued. I
> preferred this website but they stopped receiving new data sets - or
> at least they do not reply to my emails for more than a year. I am
> worried that the website will disappear and also all the uploaded
> data sets will be gone...
> Cheers,
> Martin
> 
> On 12/06/2024 20:44, John R Helliwell
>   wrote:
> 
>  cite="mid:025c572c-c078-40d5-9fca-e697aba6b...@gmail.com">
>   Dear Colleagues,
> Our article on this topic, which I imagine will be of keen interest, 
> published this afternoon, is available open access from this weblink:-
>  href="https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html;>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
> Best wishes,
> John
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[John R Helliwell]

Dear Gerard,
Quite so. But, as this CCP4bb has also observed in emails about a month ago, 
there is currently no news of proteindiffraction.org to share. 
Certainly detailed reports of its excellent work were presented at IUCr 
Melbourne. 
Greetings,
John 

Emeritus Professor John R Helliwell DSc




> On 13 Jun 2024, at 19:27, Gerard Bricogne  wrote:
> Dear John,
> 
> Is this not a matter on which internal communication within the IUCr's
> CommDat (https://www.iucr.org/resources/data/commdat) would be expected to
> be able to throw some light?
> 
> Best wishes,
> 
>Gerard
> 
> --
> On Thu, Jun 13, 2024 at 10:58:54AM +0100, John R Helliwell wrote:
>> Dear 
>> Martin,Thankyou.Unfortunately I have no explanation to offer 
>> on> href="https://proteindiffraction.org/;>proteindiffraction.org 
>> currently.Greetings,John> dir="ltr">Emeritus Professor John R Helliwell 
>> DSc> dir="ltr">On 13 Jun 2024, at 10:41, Martin Malý 
>> martin.maly...@email.cz wrote:> type="cite">
>> 
>> 
>>
>> 
>> 
>>Dear John,
>>Thank you for the link. It would be great if
>>> href="https://proteindiffraction.org/;>https://proteindiffraction.org/ 
>> (IRRMC) was rescued. I
>>preferred this website but they stopped receiving new data sets - or
>>at least they do not reply to my emails for more than a year. I am
>>worried that the website will disappear and also all the uploaded
>>data sets will be gone...
>>Cheers,
>>Martin
>>
>>On 12/06/2024 20:44, John R Helliwell
>>  wrote:
>>
>>> cite="mid:025c572c-c078-40d5-9fca-e697aba6b...@gmail.com">
>>  Dear Colleagues,
>> Our article on this topic, which I imagine will be of keen interest, 
>> published this afternoon, is available open access from this weblink:-
>> > href="https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html;>https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
>> Best wishes,
>> John
>> Emeritus Professor John R Helliwell DSc
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[John R Helliwell]

Title: Page Title
Dear Filipe,That is great to have your confirmation about cxidb.org’s ongoing activities with raw diffraction data archiving especially for SFX datasets.I have to apologise to you that your fine work is not credited in our Table 1.At IUCr Calgary Congress in 2026 I am aware of developing plans that the IUCr Committee on Data will review this landscape under its new Chairman Prof Simon Coles. It would be great if you would be there.All best wishes,JohnEmeritus Professor John R Helliwell DScOn 13 Jun 2024, at 18:11, Filipe Maia  wrote:




Hi,


https://cxidb.org is also an alternative, especially for SFX datasets.


Cheers,
Filipe



On Thu, 13 Jun 2024 at 12:48, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:


Hi

Presumably Wladek would know about this - I believe that he is an occasional visitor to this BB!

Harry

> On 13 Jun 2024, at 10:40, Martin Malý  wrote:
>
> Dear John,
> Thank you for the link. It would be great if 
https://proteindiffraction.org/ (IRRMC) was rescued. I preferred this website but they stopped receiving new data sets - or at least they do not reply to my emails for more than a year. I am worried that the website will disappear and also all the uploaded
 data sets will be gone...
> Cheers,
> Martin
>
> On 12/06/2024 20:44, John R Helliwell wrote:
>> Dear Colleagues,
>> Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:-
>>
>> 
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
>>
>> Best wishes,
>> John
>> Emeritus Professor John R Helliwell DSc
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>>
>> 
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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Filipe Maia]

Hi,

https://cxidb.org is also an alternative, especially for SFX datasets.

Cheers,
Filipe

On Thu, 13 Jun 2024 at 12:48, Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi

Presumably Wladek would know about this - I believe that he is an occasional 
visitor to this BB!

Harry

> On 13 Jun 2024, at 10:40, Martin Malý 
> mailto:martin.maly...@email.cz>> wrote:
>
> Dear John,
> Thank you for the link. It would be great if https://proteindiffraction.org/ 
> (IRRMC) was rescued. I preferred this website but they stopped receiving new 
> data sets - or at least they do not reply to my emails for more than a year. 
> I am worried that the website will disappear and also all the uploaded data 
> sets will be gone...
> Cheers,
> Martin
>
> On 12/06/2024 20:44, John R Helliwell wrote:
>> Dear Colleagues,
>> Our article on this topic, which I imagine will be of keen interest, 
>> published this afternoon, is available open access from this weblink:-
>>
>> https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
>>
>> Best wishes,
>> John
>> Emeritus Professor John R Helliwell DSc
>>
>> 
>>
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>>
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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Harry Powell]

Hi

Presumably Wladek would know about this - I believe that he is an occasional 
visitor to this BB!

Harry

> On 13 Jun 2024, at 10:40, Martin Malý  wrote:
> 
> Dear John,
> Thank you for the link. It would be great if https://proteindiffraction.org/ 
> (IRRMC) was rescued. I preferred this website but they stopped receiving new 
> data sets - or at least they do not reply to my emails for more than a year. 
> I am worried that the website will disappear and also all the uploaded data 
> sets will be gone...
> Cheers,
> Martin
> 
> On 12/06/2024 20:44, John R Helliwell wrote:
>> Dear Colleagues,
>> Our article on this topic, which I imagine will be of keen interest, 
>> published this afternoon, is available open access from this weblink:-
>> 
>> https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
>> 
>> Best wishes,
>> John
>> Emeritus Professor John R Helliwell DSc
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> 
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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[John R Helliwell]

Dear Martin,Thankyou.Unfortunately I have no explanation to offer on proteindiffraction.org currently. Greetings,John Emeritus Professor John R Helliwell DScOn 13 Jun 2024, at 10:41, Martin Malý  wrote:

  

  
  
Dear John,
Thank you for the link. It would be great if
https://proteindiffraction.org/ (IRRMC) was rescued. I
preferred this website but they stopped receiving new data sets - or
at least they do not reply to my emails for more than a year. I am
worried that the website will disappear and also all the uploaded
data sets will be gone...
Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell
  wrote:


  Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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Re: [ccp4bb] (IUCr) The evolution of raw data archiving and the growth of its importance in crystallography

[Martin Malý]

Dear John,
Thank you for the link. It would be great if 
https://proteindiffraction.org/ (IRRMC) was rescued. I preferred this 
website but they stopped receiving new data sets - or at least they do 
not reply to my emails for more than a year. I am worried that the 
website will disappear and also all the uploaded data sets will be gone...

Cheers,
Martin

On 12/06/2024 20:44, John R Helliwell wrote:

Dear Colleagues,
Our article on this topic, which I imagine will be of keen interest, published 
this afternoon, is available open access from this weblink:-
https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html
Best wishes,
John
Emeritus Professor John R Helliwell DSc



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Re: [ccp4bb] help with wwPDB validation warning

[Kay Diederichs]

Dear Gerard,

I disagree in two points with what you write:

On Mon, 10 Jun 2024 19:15:43 +0100, Gerard Bricogne  
wrote:
...
> Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense
>whatsoever in statistical terms. It must be a relic of a quantity that may
>have seemed like a good idea to someone at some stage, and has since been
>dutifully carried along forever after, and "gold-plated" so as to still be
>present in the latest revision of the mmCIF dictionary.

The quantity I_avg/sigI_avg (= /) makes as much sense in statistical 
terms as does Mn(I/sigI) (=).
As I said, numerically they are often similar (within 20% or so), in particular 
at high resolution.
IIRC, SCALEPACK (from the HKL package) prints out / (or used to print 
it out; maybe this has changed).
So there might be a reference to the usage of "I_avg/sigI_avg".

>
> Perhaps you could request a reference to the publication in which this
>quantity was proposed as a validation criterion and its acceptable limits
>were derived :-) .
>
> This being said, if it is indeed the case that the average value of
>your intensities is smaller than the average of their standard deviations,
>there is definitely something wrong somewhere. Perhaps a confusion between
>columns containing values pertaining to intensities vs. amplitudes?

There is nothing wrong if "the average value of your intensities is smaller 
than the average of their standard deviations",
if the warning that Aline reports refers to the outer shell. If it refers to 
the whole dataset, yes then there's something wrong.

Best wishes,
Kay



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Re: [ccp4bb] help with wwPDB validation warning

[Ezra Peisach]

Ok - I have tracked down where it is coming from.

The value being reported is sum(I)/sum(sigma_I).   This is not the same 
as Mean(I/sigmaI) - as I interpret the later as (Sum(I/sigma))/n.


Where I comes from is the intensity_meas, intensity_meas_au, or 
intensity column - whichever is present (priority left to right).


No averages here.

It is a simple diagnostic >80 or < 2 - report a warning.

This is from the old sf_convert program (written > 15 years ago) and the 
various warnings were carried over to a re-implementation in python.


At the time the program was implemented, the PDB had only started trying 
to make sense of the experimental data provided by the authors.  
Remember, experimental X-ray data were not required by the PDB until 
2008. Prior to that the data were optional, and some are a mess.  Use of 
experimental data in validation came afterwards.  MTZ files might have 
been accepted back then (I cannot remember) - so ensuring that the 
conversion did not result in incorrect translation was important.


The person doing the work at the time was a structural biologist, but 
may have come up with his own analyses to find conversion issues.  There 
will likely not be a reference.  Certainly the sources do not reference 
a methodology here.


So - what can we do moving forward?  Using community standards for 
identification of such errors should be incorporated. Changing the code 
is relatively easy.  Choosing the correct formulas would be the most 
meaningful.  And if sf_convert reports different data from AIMLESS - we 
should strive to understand why.



Ezra




On 6/10/24 2:15 PM, Gerard Bricogne wrote:

Dear Aline,

  This is an intriguing message: by what exact piece of software was it
produced?

  The notation I_avg/sigI_avg does not appear in the definition of the
closest item in the mmCIF dictionary, which would be

_reflns_shell.meanI_over_sigI_obs

that can be found at

https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns_shell.meanI_over_sigI_obs.html

  As Kay explained, the quantity for which you are getting a warning is a
ratio of averages, which is not at all the same as the usual average of
(signal-to-noise) ratios, denoted Mean((I)/sd(I)) in AIMLESS.

  Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense
whatsoever in statistical terms. It must be a relic of a quantity that may
have seemed like a good idea to someone at some stage, and has since been
dutifully carried along forever after, and "gold-plated" so as to still be
present in the latest revision of the mmCIF dictionary.

  Perhaps you could request a reference to the publication in which this
quantity was proposed as a validation criterion and its acceptable limits
were derived :-) .

  This being said, if it is indeed the case that the average value of
your intensities is smaller than the average of their standard deviations,
there is definitely something wrong somewhere. Perhaps a confusion between
columns containing values pertaining to intensities vs. amplitudes?

  To sober me up from all this speculation, Clemens Vonrhein tells me
that it is very likely that it is not the I_avg/sigI_avg quantity that is
actually being calculated, and that it is simply a "normal" quantity (e.g.
Mean((I)/sd(I)) that is being mis-described in the warning message.


  With best wishes,

   Gerard.

--
On Fri, Jun 07, 2024 at 03:03:30PM +0100, Aline Dias da Purificação wrote:

Dear all,

I am currently validating a structure for deposition in the wwPDB and 
encountered the following warning in the validation system:

Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo in 
SF file).

The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I didn't 
understand the warning.

Has anyone experienced this before and could assist me?

Thank you.



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Re: [ccp4bb] help with wwPDB validation warning

[Gerard Bricogne]

Dear Aline,

 This is an intriguing message: by what exact piece of software was it
produced? 

 The notation I_avg/sigI_avg does not appear in the definition of the
closest item in the mmCIF dictionary, which would be

   _reflns_shell.meanI_over_sigI_obs

that can be found at 

https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns_shell.meanI_over_sigI_obs.html

 As Kay explained, the quantity for which you are getting a warning is a
ratio of averages, which is not at all the same as the usual average of
(signal-to-noise) ratios, denoted Mean((I)/sd(I)) in AIMLESS. 

 Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense
whatsoever in statistical terms. It must be a relic of a quantity that may
have seemed like a good idea to someone at some stage, and has since been
dutifully carried along forever after, and "gold-plated" so as to still be
present in the latest revision of the mmCIF dictionary. 

 Perhaps you could request a reference to the publication in which this
quantity was proposed as a validation criterion and its acceptable limits
were derived :-) .

 This being said, if it is indeed the case that the average value of
your intensities is smaller than the average of their standard deviations,
there is definitely something wrong somewhere. Perhaps a confusion between
columns containing values pertaining to intensities vs. amplitudes?

 To sober me up from all this speculation, Clemens Vonrhein tells me
that it is very likely that it is not the I_avg/sigI_avg quantity that is
actually being calculated, and that it is simply a "normal" quantity (e.g.
Mean((I)/sd(I)) that is being mis-described in the warning message.


 With best wishes,

  Gerard.

--
On Fri, Jun 07, 2024 at 03:03:30PM +0100, Aline Dias da Purificação wrote:
> Dear all,
> 
> I am currently validating a structure for deposition in the wwPDB and 
> encountered the following warning in the validation system: 
> 
> Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo 
> in SF file). 
> 
> The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I didn't 
> understand the warning.
> 
> Has anyone experienced this before and could assist me?
> 
> Thank you.
> 
> 
> 
> 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 
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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] Coot 1.1 General Tools

[Simon Vecchioni]

Lucrezia,

Thanks for your help!

1) This works very well -- thanks for pointing me in the right direction.

2) Thanks

3) When I do this, no anchor appears. There's a "no intermediate atoms"
error, with a 0x0 matrix of fixed atoms. Maybe it's a DNA refinement error?

Cheers

On Mon, Jun 3, 2024 at 1:15 PM lucrezia catapano 
wrote:

> Dear Simon,
>
> 1. The new clipping keybindings are ‘1’ and ‘2’ for clipping front and ‘3’
> and ‘4’ for clipping back (like in Moorhen as well). You can find them in
> ‘About’- ’Shortcuts' (page 2 to be precise).
> 2. We need to fix this (about a week)
> 3. You center on an atom, then click on ‘Fixed atom’ on the right vertical
> toolbar, then ‘Fix atom’, and an ‘anchor’ marker will appear. Then it
> should work.
>
> Regards
> Lucrezia
>
>
> Lucrezia Catapano
> Postdoctoral Scientist, Murshudov Group
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue,
> Cambridge CB2 0QH, UK.
> lucre...@mrc-lmb.cam.ac.uk
>
>
>
> On 3 Jun 2024, at 17:14, Simon Vecchioni  wrote:
>
> CAUTION: This email originated from outside of the LMB:
> *.-owner-ccp...@jiscmail.ac.uk-.*
> Do not click links or open attachments unless you recognize the sender and
> know the content is safe.
> If you think this is a phishing email, please forward it to
> phish...@mrc-lmb.cam.ac.uk
>
>
> --
> Paul and CCP4 Community,
>
> Emailing the larger listserv because some of these might be useful to all.
> Thanks for the updates to the latest build.
>
> 1) In Coot 1.1.08, the graphics are fantastic! I've been struggling to
> clip the view for figure building. In old Coot, there was a "d" and "f"
> keyset that would toggle the fill/depth. Now there are other commands tied
> to "d" and nearby keys. Is there a menu that contains this feature, or a
> way to edit key bindings? I've experimented with the graphics menus but
> don't know the name of the feature I'm looking for.
>
> 2) Saving symmetry coordinates used to be a click operation, but now the
> interface has moved away from click selection. I haven't successfully been
> able to save a symmetry state--is there a good way to do this now?
>
> 3) Fix/Unfix atom also ran on click--I can go to a particular atom using
> the GUI, but I haven't been successful in fixing that atom for refinement.
>
> Thanks for your advice and assistance,
> Simon
>
> --
> Simon Vecchioni [he/his]
> Postdoctoral Researcher
> NYU Chemistry
>
> --
>
> 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] help with wwPDB validation warning

[Kay Diederichs]

Hi Aline,

I see nothing wrong with / being 0.83

Mean((I)/sd(I)) is , which is not the same as / so you cannot 
expect the numerical values to be the same (even in case the resolution shell 
definition is identical), although the two values usually do not differ much. 
Take for example two reflections, I1=100 sigI1=20 and I2=200 sigI2=10. Then 
=(5+20)/2=12.5 and /=150/15=10 .

Best,
Kay


On Fri, 7 Jun 2024 15:03:30 +0100, Aline Dias da Purificação 
 wrote:

>Dear all,
>
>I am currently validating a structure for deposition in the wwPDB and 
>encountered the following warning in the validation system: 
>
>Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo 
>in SF file). 
>
>The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I didn't 
>understand the warning.
>
>Has anyone experienced this before and could assist me?
>
>Thank you.
>
>
>
>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/



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Re: [ccp4bb] help with wwPDB validation warning

[Eleanor Dodson]

Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2
Eleanor

On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação <
d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear all,
>
> I am currently validating a structure for deposition in the wwPDB and
> encountered the following warning in the validation system:
>
> Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or
> SigIo in SF file).
>
> The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShell, so I
> didn't understand the warning.
>
> Has anyone experienced this before and could assist me?
>
> Thank you.
>
> 
>
> 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/
>



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Re: [ccp4bb] Key bindings WinCoot 0.9

[Bernhard Lohkamp]

This (.coot-preferences) is where the key bindings script should be 
installed to (*). Not sure why it didnt happen in your case. I assume 
some permission issue. Difficult to say from your description. Anyway, 
good that it works now.


B

(*) which actually resides in %COOT_HOME% which by default is your coot 
installation directory i.e. (default) C:\WinCoot. This is defined in 
wincoot.bat. Maybe your admin has changed things there...


On 06/06/2024 15:28, Misbha Ud Din Ahmad wrote:

Thanks Jasmin and Lucrezia for this suggestion.
I realized that the best way is to save this script in the 
.coot-preferences folder. In that case you don't have to run the script 
every time you start a new Coot session.


Best regards
Misbha

On Thu, Jun 6, 2024 at 3:08 PM lucrezia catapano 
mailto:lucre...@mrc-lmb.cam.ac.uk>> wrote:


Dear Misbha,

Download this script and try Calculate-Run script
preview.png
template_key_bindings


Text Document · 8 KB






Lucrezia
Lucrezia Catapano
Postdoctoral Scientist, Murshudov Group
MRC Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge CB2 0QH, UK.
lucre...@mrc-lmb.cam.ac.uk 




On 6 Jun 2024, at 12:52, Misbha Ud Din Ahmad
mailto:misba.ah...@gmail.com>> wrote:

CAUTION: This email originated from outside of the LMB:
*.-owner-ccp...@jiscmail.ac.uk-.*
Do not click links or open attachments unless you recognize the
sender and know the content is safe.
If you think this is a phishing email, please forward it to
phish...@mrc-lmb.cam.ac.uk 


--

Dear all,
We are experiencing issues with installing key bindings in WinCoot
0.9.8.93 EL. There are simply no buttons displayed for this option.

The key binding buttons were at least visible once and could be
installed when executing WinCoot from a Windows admin account, but
we couldn't reproduce the result a second time.
In our organization, the software is installed by the admin and we
get access to it from our user accounts.
For the record, we didn't encounter these issues in the previous
0.8 WinCoot versions.
Is there a workaround for getting this fixed?

Thanks in advance.

Best
Misbha



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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

[Eleanor Dodson]

Well, REFMAC output a (mislabelled)  F SIGF which was detwinned so if you
deposited the REFMAC output I guess that is detwinned..
Do you have the original REFMAC input still?
Eleanor

On Thu, 6 Jun 2024 at 15:18, Ben Bax  wrote:

> Hi,
>   I am just re-refining an old twinned dataset - which I will
> redeposit (refinement is never finished).
> The pdb seem to have automagically detwinned my data.
> Where do I find my original twinned data (F and SIGF)? (or will I have
> to redeposit my original un-detwinned structure factors).
>  Thanks, Ben
>
>
>
> On Fri, May 31, 2024 at 4:36 PM Ezra Peisach
>  wrote:
> >
> > In fall of 2024, electron density map coefficients will be available in
> > the public PDB archive for all X-ray structures. These map coefficients
> > will be the same as used in wwPDB Validation Reports.
> >
> > The new map coefficients files will replace the electron density maps
> > and combined map coefficient files calculated and distributed by RCSB
> > PDB and used by the NGLviewer at RCSB.org. These data (served by
> > EDMAPS.rcsb.org) are calculated using publicly-available coordinate
> > files and structure factor files and offered in DSN6 formatted map files
> > and MTZ formatted map coefficient files. RCSB PDB plans to shutdown the
> > NGL viewer by July 2024
> > (https://www.rcsb.org/news/feature/65b42d3fc76ca3abcc925d15) and will no
> > longer need the data served by EDMAPS.rcsb.org.
> >
> > RCSB PDB will be phasing out EDMAPS.rcsb.org:
> >
> >   *  June 28, 2024: DSN6-formatted map files will no longer be
> > provided. EDMAPS.rcsb.org will only serve MTZ files with map
> coefficients.
> >   *  Fall 2024: Electron density map coefficients will be available
> > in the public PDB archive for all X-ray structures. At this point,
> > EDMAPS.rcsb.org will be shut down, including access to MTZ files with
> > map coefficients from this service.
> >
> > To help users with this transition, RCSB PDB will be holding a Virtual
> > Office Hour on Thursday June 13, 2024 from 1:00pm-2:00pm Eastern,
> > 10:00am-11am Pacific. Please register online for this event at
> > https://go.rutgers.edu/psx4pr63.
> >
> > Questions about this transition or the Virtual Office Hour can be sent
> > to i...@rcsb.org.
> >
> > 
> >
> > 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
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>
> 
>
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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

[Deborah Harrus]

Dear Jon,

We will continue to serve the maps and are looking into updating the 
process to use the map coefficients now available in the wwPDB FTP data 
to make the maps compatible with the validation process.


Kind regards,

Deborah Harrus

PDBe

On 01/06/2024 14:28, Jon Cooper wrote:

It would be interesting to know if this will affect the the electron density 
maps which are downloadable from the EBI:

www.ebi.ac.uk/pdbe

They don't currently serve the older dsn6 format, only ccp4, I think.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 31/05/2024 16:36, Ezra Peisach 
 wrote:


  In fall of 2024, electron density map coefficients will be available in
  the public PDB archive for all X-ray structures. These map coefficients
  will be the same as used in wwPDB Validation Reports.
  
  The new map coefficients files will replace the electron density maps

  and combined map coefficient files calculated and distributed by RCSB
  PDB and used by the NGLviewer at RCSB.org. These data (served by
  EDMAPS.rcsb.org) are calculated using publicly-available coordinate
  files and structure factor files and offered in DSN6 formatted map files
  and MTZ formatted map coefficient files. RCSB PDB plans to shutdown the
  NGL viewer by July 2024
  (https://www.rcsb.org/news/feature/65b42d3fc76ca3abcc925d15) and will no
  longer need the data served by EDMAPS.rcsb.org.
  
  RCSB PDB will be phasing out EDMAPS.rcsb.org:
  
    *  June 28, 2024: DSN6-formatted map files will no longer be

  provided. EDMAPS.rcsb.org will only serve MTZ files with map coefficients.
    *  Fall 2024: Electron density map coefficients will be available
  in the public PDB archive for all X-ray structures. At this point,
  EDMAPS.rcsb.org will be shut down, including access to MTZ files with
  map coefficients from this service.
  
  To help users with this transition, RCSB PDB will be holding a Virtual

  Office Hour on Thursday June 13, 2024 from 1:00pm-2:00pm Eastern,
  10:00am-11am Pacific. Please register online for this event at
  https://go.rutgers.edu/psx4pr63.
  
  Questions about this transition or the Virtual Office Hour can be sent

  to i...@rcsb.org.
  
  
  
  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/
  



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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

[Ben Bax]

Hi,
  I am just re-refining an old twinned dataset - which I will
redeposit (refinement is never finished).
The pdb seem to have automagically detwinned my data.
Where do I find my original twinned data (F and SIGF)? (or will I have
to redeposit my original un-detwinned structure factors).
 Thanks, Ben



On Fri, May 31, 2024 at 4:36 PM Ezra Peisach
 wrote:
>
> In fall of 2024, electron density map coefficients will be available in
> the public PDB archive for all X-ray structures. These map coefficients
> will be the same as used in wwPDB Validation Reports.
>
> The new map coefficients files will replace the electron density maps
> and combined map coefficient files calculated and distributed by RCSB
> PDB and used by the NGLviewer at RCSB.org. These data (served by
> EDMAPS.rcsb.org) are calculated using publicly-available coordinate
> files and structure factor files and offered in DSN6 formatted map files
> and MTZ formatted map coefficient files. RCSB PDB plans to shutdown the
> NGL viewer by July 2024
> (https://www.rcsb.org/news/feature/65b42d3fc76ca3abcc925d15) and will no
> longer need the data served by EDMAPS.rcsb.org.
>
> RCSB PDB will be phasing out EDMAPS.rcsb.org:
>
>   *  June 28, 2024: DSN6-formatted map files will no longer be
> provided. EDMAPS.rcsb.org will only serve MTZ files with map coefficients.
>   *  Fall 2024: Electron density map coefficients will be available
> in the public PDB archive for all X-ray structures. At this point,
> EDMAPS.rcsb.org will be shut down, including access to MTZ files with
> map coefficients from this service.
>
> To help users with this transition, RCSB PDB will be holding a Virtual
> Office Hour on Thursday June 13, 2024 from 1:00pm-2:00pm Eastern,
> 10:00am-11am Pacific. Please register online for this event at
> https://go.rutgers.edu/psx4pr63.
>
> Questions about this transition or the Virtual Office Hour can be sent
> to i...@rcsb.org.
>
> 
>
> 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] Resampling CryoEM Density map to XRD Density map for Difference Map

[Devbrat Kumar]

Dear Paul,

Thank you

Regards
Devbrat

On Thu, Jun 6, 2024, 8:53 AM Paul Emsley  wrote:

>
> On 06/06/2024 04:00, Devbrat Kumar wrote:
>
>
> --
> Dear Paul,
>
> Thank you for your response. I wanted to compare a Coulomb potential map
> to an electron density map. Before aligning these maps, I need to bring
> them to similar parameters, which requires rescaling one map to match the
> other. After that, I can proceed with density subtraction.
>
> I hope this clarifies my query. Sorry for any confusion.
> Thank you again.
> Regards
> Devbrat
>
>
> On Wed, Jun 5, 2024, 7:56 PM Paul Emsley 
> wrote:
>
>>
>> On 05/06/2024 07:00, Devbrat Kumar wrote:
>>
>>
>> --
>>
>> Hello Everyone,
>>
>> Hello Devbrat,
>>
>> I have a query regarding the resampling of cryoEM density to match
>> crystal density to obtain a density difference map. Specifically, I am
>> trying to determine if it is feasible to resample a cryoEM map with an XRD
>> density map. However, each time I attempt this, the resampling output
>> provides an arbitrary ASU resample map, resulting in a significant loss of
>> major density.
>>
>> I have been using Coot and Chimera for this process but have not achieved
>> the desired outcome. Please guide me or suggest how to move forward with
>> this. My goal is to create an accurate final density difference map.
>>
>>
>> It is not clear to me exactly what the problem is.
>>
>> In Coot speak, "resampling" is (merely) changing the grid sampling so
>> that the map appears (typically) on a finer grid.
>>
>> I don't think that this is what you want.
>>
>> You want is, I think, "Transform Map by LSQ Model-fit" and if that is
>> what you used, then I can't help until I am more clear about what you think
>> has gone wrong.
>>
>> Regards,
>>
>> Paul.
>>
>> Ah, OK, so you want to *rescale* not resample. The tool (in our world) to
> do that is EMDA (available in CCPEM).
>
> Paul.
>
>
>
> --
>
> 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] Resampling CryoEM Density map to XRD Density map for Difference Map

[Paul Emsley]

On 06/06/2024 04:00, Devbrat Kumar wrote:



--

Dear Paul,

Thank you for your response. I wanted to compare a Coulomb potential 
map to an electron density map. Before aligning these maps, I need to 
bring them to similar parameters, which requires rescaling one map to 
match the other. After that, I can proceed with density subtraction.


I hope this clarifies my query. Sorry for any confusion.
Thank you again.
Regards
Devbrat


On Wed, Jun 5, 2024, 7:56 PM Paul Emsley  
wrote:



On 05/06/2024 07:00, Devbrat Kumar wrote:



--

Hello Everyone,


Hello Devbrat,


I have a query regarding the resampling of cryoEM density to
match crystal density to obtain a density difference map.
Specifically, I am trying to determine if it is feasible to
resample a cryoEM map with an XRD density map. However, each time
I attempt this, the resampling output provides an arbitrary ASU
resample map, resulting in a significant loss of major density.

I have been using Coot and Chimera for this process but have not
achieved the desired outcome. Please guide me or suggest how to
move forward with this. My goal is to create an accurate final
density difference map.




It is not clear to me exactly what the problem is.

In Coot speak, "resampling" is (merely) changing the grid sampling
so that the map appears (typically) on a finer grid.

I don't think that this is what you want.

You want is, I think, "Transform Map by LSQ Model-fit" and if that
is what you used, then I can't help until I am more clear about
what you think has gone wrong.

Regards,

Paul.


Ah, OK, so you want to *rescale* not resample. The tool (in our world) 
to do that is EMDA (available in CCPEM).


Paul.




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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Devbrat Kumar]

Dear Paul,

Thank you for your response. I wanted to compare a Coulomb potential map to
an electron density map. Before aligning these maps, I need to bring them
to similar parameters, which requires rescaling one map to match the other.
After that, I can proceed with density subtraction.

I hope this clarifies my query. Sorry for any confusion.
Thank you again.
Regards
Devbrat


On Wed, Jun 5, 2024, 7:56 PM Paul Emsley  wrote:

>
> On 05/06/2024 07:00, Devbrat Kumar wrote:
>
>
> --
>
> Hello Everyone,
>
> Hello Devbrat,
>
> I have a query regarding the resampling of cryoEM density to match crystal
> density to obtain a density difference map. Specifically, I am trying to
> determine if it is feasible to resample a cryoEM map with an XRD density
> map. However, each time I attempt this, the resampling output provides an
> arbitrary ASU resample map, resulting in a significant loss of major
> density.
>
> I have been using Coot and Chimera for this process but have not achieved
> the desired outcome. Please guide me or suggest how to move forward with
> this. My goal is to create an accurate final density difference map.
>
>
> It is not clear to me exactly what the problem is.
>
> In Coot speak, "resampling" is (merely) changing the grid sampling so that
> the map appears (typically) on a finer grid.
>
> I don't think that this is what you want.
>
> You want is, I think, "Transform Map by LSQ Model-fit" and if that is what
> you used, then I can't help until I am more clear about what you think has
> gone wrong.
>
> Regards,
>
> Paul.
>
>
>
> --
>
> 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] Resampling CryoEM Density map to XRD Density map for Difference Map

[Devbrat Kumar]

Dear Jon

I will keep this in mind while working on it.

Thank you.
Regards
Devbrat

On Wed, Jun 5, 2024, 7:11 PM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Another factor might be that ccpem uses a different axis order to gemmi
> and ccp4 ;-0
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>
>  Original Message 
> On 05/06/2024 12:51, Guillaume Gaullier wrote:
>
> With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in
> real space (this is trivial to do interactively in ChimeraX) rather than by
> MR.
> --
> *From:* CCP4 bulletin board  on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Wednesday, June 5, 2024 1:39:56 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map
> for Difference Map
>
> Hmm - rather tricky! I would do an MR search with the crystal model v the
> EM density,
> Steps would be:
> 1) convert EM density to "structure factors". - there are tools which do
> this ..
>   1a) You need to go back to ccp4i - program sfall to read map to generate
> SFs from map - then cad or sftools to add a fake SigF column
> 2) Solve MR search with the model v these "structure factors" using them
> as Fobs
> 3) Calculate the structure factors from the MR positiooned model and get
> the difference map..
>
>
> On Wed, 5 Jun 2024 at 11:46, Martin Malý  wrote:
>
>> Dear Devbrat,
>>
>> I am now playing with a similar problem but I don't have a simple
>> solution for you as I'm also quite stuck. You can check these software
>> tools which involve some scripting in Python (NumPy, SciPy) and C++:
>>
>> EMDA (for cryoEM maps, included in CCP-EM)
>> https://gitlab.com/ccpem/emda
>> https://doi.org/10.1016/j.jsb.2021.107826
>>
>> Gemmi (mainly for crystallography, included in CCP4)
>> https://gemmi.readthedocs.io/en/latest/grid.html
>>
>> Maybe there are also some relevant features in CCTBX (included in CCP4
>> and Phenix).
>>
>> Cheers,
>> Martin
>>
>> On 05/06/2024 07:00, Devbrat Kumar wrote:
>>
>> Hello Everyone,
>>
>> Greetings!
>>
>> I have a query regarding the resampling of cryoEM density to match
>> crystal density to obtain a density difference map. Specifically, I am
>> trying to determine if it is feasible to resample a cryoEM map with an XRD
>> density map. However, each time I attempt this, the resampling output
>> provides an arbitrary ASU resample map, resulting in a significant loss of
>> major density.
>>
>> I have been using Coot and Chimera for this process but have not achieved
>> the desired outcome. Please guide me or suggest how to move forward with
>> this. My goal is to create an accurate final density difference map.
>>
>> Thank you in advance for your help.
>> *Warm Regards-*
>> *Devbrat Kumar*
>>
>>
>> --
>>
>> 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:
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>
>
> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner
> igen avsändaren och vet att innehållet är säkert.
> CAUTION: Do not click on links or open attachments unless you recognise
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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Devbrat Kumar]

Dear Guillaume

I will keep that in mind while trying.

Thank you
Regards
Devbrat

On Wed, Jun 5, 2024, 5:21 PM Guillaume Gaullier <
guillaume.gaull...@kemi.uu.se> wrote:

> With a cryoEM map, it's easier to do the rigid-body fitting of step 2 in
> real space (this is trivial to do interactively in ChimeraX) rather than by
> MR.
> --
> *From:* CCP4 bulletin board  on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Wednesday, June 5, 2024 1:39:56 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map
> for Difference Map
>
> Hmm - rather tricky! I would do an MR search with the crystal model v the
> EM density,
> Steps would be:
> 1) convert EM density to "structure factors". - there are tools which do
> this ..
>   1a) You need to go back to ccp4i - program sfall to read map to generate
> SFs from map - then cad or sftools to add a fake SigF column
> 2) Solve MR search with the model v these "structure factors" using them
> as Fobs
> 3) Calculate the structure factors from the MR positiooned model and get
> the difference map..
>
>
> On Wed, 5 Jun 2024 at 11:46, Martin Malý  wrote:
>
>> Dear Devbrat,
>>
>> I am now playing with a similar problem but I don't have a simple
>> solution for you as I'm also quite stuck. You can check these software
>> tools which involve some scripting in Python (NumPy, SciPy) and C++:
>>
>> EMDA (for cryoEM maps, included in CCP-EM)
>> https://gitlab.com/ccpem/emda
>> https://doi.org/10.1016/j.jsb.2021.107826
>>
>> Gemmi (mainly for crystallography, included in CCP4)
>> https://gemmi.readthedocs.io/en/latest/grid.html
>>
>> Maybe there are also some relevant features in CCTBX (included in CCP4
>> and Phenix).
>>
>> Cheers,
>> Martin
>>
>> On 05/06/2024 07:00, Devbrat Kumar wrote:
>>
>> Hello Everyone,
>>
>> Greetings!
>>
>> I have a query regarding the resampling of cryoEM density to match
>> crystal density to obtain a density difference map. Specifically, I am
>> trying to determine if it is feasible to resample a cryoEM map with an XRD
>> density map. However, each time I attempt this, the resampling output
>> provides an arbitrary ASU resample map, resulting in a significant loss of
>> major density.
>>
>> I have been using Coot and Chimera for this process but have not achieved
>> the desired outcome. Please guide me or suggest how to move forward with
>> this. My goal is to create an accurate final density difference map.
>>
>> Thank you in advance for your help.
>> *Warm Regards-*
>> *Devbrat Kumar*
>>
>>
>> --
>>
>> 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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>
>
> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner
> igen avsändaren och vet att innehållet är säkert.
> CAUTION: Do not click on links or open attachments unless you recognise
> the sender and know the content is safe.
>
>
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
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> data. For more information on how this is performed, please read here:
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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Devbrat Kumar]

Hello Eleanor,

Thank you for your consistent response to my inquiry. I will follow your
suggestions and willl tell you the updates.


Regards
Devbrat

On Wed, Jun 5, 2024, 5:10 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hmm - rather tricky! I would do an MR search with the crystal model v the
> EM density,
> Steps would be:
> 1) convert EM density to "structure factors". - there are tools which do
> this ..
>   1a) You need to go back to ccp4i - program sfall to read map to generate
> SFs from map - then cad or sftools to add a fake SigF column
> 2) Solve MR search with the model v these "structure factors" using them
> as Fobs
> 3) Calculate the structure factors from the MR positiooned model and get
> the difference map..
>
>
> On Wed, 5 Jun 2024 at 11:46, Martin Malý  wrote:
>
>> Dear Devbrat,
>>
>> I am now playing with a similar problem but I don't have a simple
>> solution for you as I'm also quite stuck. You can check these software
>> tools which involve some scripting in Python (NumPy, SciPy) and C++:
>>
>> EMDA (for cryoEM maps, included in CCP-EM)
>> https://gitlab.com/ccpem/emda
>> https://doi.org/10.1016/j.jsb.2021.107826
>>
>> Gemmi (mainly for crystallography, included in CCP4)
>> https://gemmi.readthedocs.io/en/latest/grid.html
>>
>> Maybe there are also some relevant features in CCTBX (included in CCP4
>> and Phenix).
>>
>> Cheers,
>> Martin
>>
>> On 05/06/2024 07:00, Devbrat Kumar wrote:
>>
>> Hello Everyone,
>>
>> Greetings!
>>
>> I have a query regarding the resampling of cryoEM density to match
>> crystal density to obtain a density difference map. Specifically, I am
>> trying to determine if it is feasible to resample a cryoEM map with an XRD
>> density map. However, each time I attempt this, the resampling output
>> provides an arbitrary ASU resample map, resulting in a significant loss of
>> major density.
>>
>> I have been using Coot and Chimera for this process but have not achieved
>> the desired outcome. Please guide me or suggest how to move forward with
>> this. My goal is to create an accurate final density difference map.
>>
>> Thank you in advance for your help.
>> *Warm Regards-*
>> *Devbrat Kumar*
>>
>>
>> --
>>
>> 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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Re: [ccp4bb] Resampling CryoEM Density map to XRD Density map for Difference Map

[Devbrat Kumar]

Hello Martin,

Thank you for your email and I will look into it.

Regards
Devbrat


On Wed, Jun 5, 2024, 4:16 PM Martin Malý  wrote:

> Dear Devbrat,
>
> I am now playing with a similar problem but I don't have a simple solution
> for you as I'm also quite stuck. You can check these software tools which
> involve some scripting in Python (NumPy, SciPy) and C++:
>
> EMDA (for cryoEM maps, included in CCP-EM)
> https://gitlab.com/ccpem/emda
> https://doi.org/10.1016/j.jsb.2021.107826
>
> Gemmi (mainly for crystallography, included in CCP4)
> https://gemmi.readthedocs.io/en/latest/grid.html
>
> Maybe there are also some relevant features in CCTBX (included in CCP4 and
> Phenix).
>
> Cheers,
> Martin
>
> On 05/06/2024 07:00, Devbrat Kumar wrote:
>
> Hello Everyone,
>
> Greetings!
>
> I have a query regarding the resampling of cryoEM density to match crystal
> density to obtain a density difference map. Specifically, I am trying to
> determine if it is feasible to resample a cryoEM map with an XRD density
> map. However, each time I attempt this, the resampling output provides an
> arbitrary ASU resample map, resulting in a significant loss of major
> density.
>
> I have been using Coot and Chimera for this process but have not achieved
> the desired outcome. Please guide me or suggest how to move forward with
> this. My goal is to create an accurate final density difference map.
>
> Thank you in advance for your help.
> *Warm Regards-*
> *Devbrat Kumar*
>
>
> --
>
> 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] Ligand identification in X-ray density

[Artem Evdokimov]

At this resolution you should be able to infer differences between C and O
based on the map levels at each location. Another dead giveaway is the bond
lengths and the asymmetry of the top region - that is not a carboxylic acid
to me.

This looks lime MPD to me, very classic shape.

Artem

On Wed, Jun 5, 2024, 1:37 PM Jeroen Mesters <
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk> wrote:

> Oooops, correct, got my reasoning turned around too….   But it could still
> be a betain if the water is more distant… We need a different view!
>
> Best
>
> J.
> __.
> Dr. math. et dis. nat. Jeroen R. Mesters
> Biological Safety Officer (BBS)
> Deputy, Lecturer, Program Coordinator Infection Biology
> Visiting Professorship in Biophysics South Bohemian University
>
>
> [image: attachment.png]
>
>
>
> University of Lübeck
> Center for Structural and Cell Biology in Medicine
> Institute of Biochemistry
> Ratzeburger Allee 160
> 23562 Lübeck
>
> Tel +49 451 3101 3105
> https://orcid.org/-0001-8532-6699
>
> Am 05.06.2024 um 19:22 schrieb Zachary A. Wood :
>
> I sent my  last response too soon….
>
> The ‘top’ end of the molecule in the image looks more like a carboxylic
> acid accepting H-bonds from two backbone amides (supporting the betaine
> assignment, and not MPD), but the ‘bottom’ end of the molecule looks like
> it is forming an H-bond with a well-ordered water molecule. If it were
> betaine, then that end would be three methyls there (but MPD would have a
> hydroxyl there). I am starting to think it is neither…probably one of the
> organic acids in the crystallization  mix.
>
>
>
>
>
> Best regards,
>
> Z
>
>
> ***
> Zachary A. Wood, Ph.D. *(He/Him)*
> Professor and Graduate Coordinator
>
> Josiah Meigs Distinguished Teaching Professor
>
> Associate Director of SER-CAT
> Department of Biochemistry & Molecular Biology
> University of Georgia
> Life Sciences Building, Rm A426B
> 120 Green Street
> Athens, GA  30602-7229
> Office: 706-583-0304
> Lab:706-583-0303
> FAX: 706-542-1738
> *******
>
>
>
>
>
> *From: *Jeroen Mesters 
> *Date: *Wednesday, June 5, 2024 at 1:17 PM
> *To: *Zachary A. Wood 
> *Cc: *CCP4BB@jiscmail.ac.uk 
> *Subject: *Re: [ccp4bb] Ligand identification in X-ray density
>
> You don't often get email from jeroen.mest...@uni-luebeck.de. Learn why
> this is important <https://aka.ms/LearnAboutSenderIdentification>
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
> Yes!  That is why I excluded MPD as there is the water molecule close-by….
> But we need a different view….
>
>
>
> Best
>
>
>
> J.
>
> __
>
> Dr. math. et dis. nat. Jeroen R. Mesters
> Biological Safety Officer (BBS)
> Deputy, Lecturer, Program Coordinator Infection Biology
> Visiting Professorship in Biophysics South Bohemian University
> University of Lübeck
>
> Center for Structural and Cell Biology in Medicine
> Institute of Biochemistry
> Ratzeburger Allee 160
> 23562 Lübeck
>
> Tel +49 451 3101 3105
> https://orcid.org/-0001-8532-6699
>
>
>
> Am 05.06.2024 um 19:11 schrieb Zachary A. Wood <
> d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>:
>
>
>
> It is pretty well-ordered, so I would expect the H-bonding pattern to
> distinguish between betaine and MPD.
>
>
>
> Best regards,
>
> Z
>
>
> ***
> Zachary A. Wood, Ph.D. *(He/Him)*
> Professor and Graduate Coordinator
>
> Josiah Meigs Distinguished Teaching Professor
>
> Associate Director of SER-CAT
> Department of Biochemistry & Molecular Biology
> University of Georgia
> Life Sciences Building, Rm A426B
> 120 Green Street
> Athens, GA  30602-7229
> Office: 706-583-0304
> Lab:706-583-0303
> FAX: 706-542-1738
> ***
>
>
>
>
>
> *From: *CCP4 bulletin board  on behalf of Jon
> Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
> *Date: *Wednesday, June 5, 2024 at 1:01 PM
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *Re: [ccp4bb] Ligand identification in X-ray density
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
> Or, it could be MPD ;-?
>
> Best wishes, Jon Cooper.
> jon.b.coo...@protonmail.com
>
> Sent from Proton Mail Android
>
>
>
>  Original Message 
> On 05/06/2024 17:54, Jeroen Mesters <
> cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Thank you for this intriguing information!
>
>
>
> At the same time, this also implies that not a

Re: [ccp4bb] Ligand identification in X-ray density

[Jeroen Mesters]

Oooops, correct, got my reasoning turned around too….   But it could still be a 
betain if the water is more distant… We need a different view!

Best

J.
__.
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University


[attachment.png]



University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

Tel +49 451 3101 3105
https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 19:22 schrieb Zachary A. Wood :

I sent my  last response too soon….
The ‘top’ end of the molecule in the image looks more like a carboxylic acid 
accepting H-bonds from two backbone amides (supporting the betaine assignment, 
and not MPD), but the ‘bottom’ end of the molecule looks like it is forming an 
H-bond with a well-ordered water molecule. If it were betaine, then that end 
would be three methyls there (but MPD would have a hydroxyl there). I am 
starting to think it is neither…probably one of the organic acids in the 
crystallization  mix.


Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: Jeroen Mesters 
Date: Wednesday, June 5, 2024 at 1:17 PM
To: Zachary A. Wood 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Ligand identification in X-ray density

You don't often get email from jeroen.mest...@uni-luebeck.de. Learn why this is 
important<https://aka.ms/LearnAboutSenderIdentification>

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Yes!  That is why I excluded MPD as there is the water molecule close-by…. But 
we need a different view….

Best

J.
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

Tel +49 451 3101 3105
https://orcid.org/-0001-8532-6699


Am 05.06.2024 um 19:11 schrieb Zachary A. Wood 
<d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>:

It is pretty well-ordered, so I would expect the H-bonding pattern to 
distinguish between betaine and MPD.

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Ligand identification in X-ray density
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Or, it could be MPD ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com>

Sent from Proton Mail Android


 Original Message 
On 05/06/2024 17:54, Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Thank you for this intriguing information!

At the same time, this also implies that not all entities that have been 
modelled as MPD are actually MDP but could also be a betain, right!?…..

Best,

Jeroen
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 18:41 schrieb Zachary A. Wood 
mailto:z...@uga.edu>>:

Hello Everyone,

It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).

Best regards,

Z


***
Zachary A

Re: [ccp4bb] Ligand identification in X-ray density

[Zachary A. Wood]

I sent my  last response too soon….
The ‘top’ end of the molecule in the image looks more like a carboxylic acid 
accepting H-bonds from two backbone amides (supporting the betaine assignment, 
and not MPD), but the ‘bottom’ end of the molecule looks like it is forming an 
H-bond with a well-ordered water molecule. If it were betaine, then that end 
would be three methyls there (but MPD would have a hydroxyl there). I am 
starting to think it is neither…probably one of the organic acids in the 
crystallization  mix.


Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: Jeroen Mesters 
Date: Wednesday, June 5, 2024 at 1:17 PM
To: Zachary A. Wood 
Cc: CCP4BB@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Ligand identification in X-ray density
You don't often get email from jeroen.mest...@uni-luebeck.de. Learn why this is 
important<https://aka.ms/LearnAboutSenderIdentification>
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Yes!  That is why I excluded MPD as there is the water molecule close-by…. But 
we need a different view….

Best

J.
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

Tel +49 451 3101 3105
https://orcid.org/-0001-8532-6699


Am 05.06.2024 um 19:11 schrieb Zachary A. Wood 
<d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>:

It is pretty well-ordered, so I would expect the H-bonding pattern to 
distinguish between betaine and MPD.

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Ligand identification in X-ray density
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Or, it could be MPD ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com>

Sent from Proton Mail Android


 Original Message 
On 05/06/2024 17:54, Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Thank you for this intriguing information!

At the same time, this also implies that not all entities that have been 
modelled as MPD are actually MDP but could also be a betain, right!?…..

Best,

Jeroen
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 18:41 schrieb Zachary A. Wood 
mailto:z...@uga.edu>>:

Hello Everyone,

It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday,

Re: [ccp4bb] Ligand identification in X-ray density

[Jeroen Mesters]

Yes!  That is why I excluded MPD as there is the water molecule close-by…. But 
we need a different view….

Best

J.
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

Tel +49 451 3101 3105
https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 19:11 schrieb Zachary A. Wood 
<d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>:

It is pretty well-ordered, so I would expect the H-bonding pattern to 
distinguish between betaine and MPD.

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Ligand identification in X-ray density
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Or, it could be MPD ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com>

Sent from Proton Mail Android


 Original Message 
On 05/06/2024 17:54, Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Thank you for this intriguing information!

At the same time, this also implies that not all entities that have been 
modelled as MPD are actually MDP but could also be a betain, right!?…..

Best,

Jeroen
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

https://orcid.org/-0001-8532-6699


Am 05.06.2024 um 18:41 schrieb Zachary A. Wood 
mailto:z...@uga.edu>>:

Hello Everyone,

It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Ligand identification in X-ray density

You don't often get email from 
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>.
 Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi,

proteins my pick up ligands from the „source" from which they were isolated…. 
Looks to me like trimethylglycine, an amino-acid derivative found in plants…

Regards,

Jeroen
__
https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
mailto:khadijahameenk...@gmail.com>>:

Dear All,

I am a first-year PhD student in a structural biology lab. I am building a 
model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions 
for fitting a ligand in an unknown X-ray density (attached image) in the 
protein binding pocket. The details for protein purification and 
crystallization buffers are below:

Purification: NaCl, Tris-HCl pH 8.5, Glycerol
Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium 
citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, 
Precipitant (PEG3350, MPD)

I have tried 

Re: [ccp4bb] Ligand identification in X-ray density

[Zachary A. Wood]

It is pretty well-ordered, so I would expect the H-bonding pattern to 
distinguish between betaine and MPD.

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board  on behalf of Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, June 5, 2024 at 1:01 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ligand identification in X-ray density
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Or, it could be MPD ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 05/06/2024 17:54, Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk> wrote:
Thank you for this intriguing information!

At the same time, this also implies that not all entities that have been 
modelled as MPD are actually MDP but could also be a betain, right!?…..

Best,

Jeroen
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

https://orcid.org/-0001-8532-6699


Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :

Hello Everyone,

It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Ligand identification in X-ray density
You don't often get email from 
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>.
 Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi,

proteins my pick up ligands from the „source" from which they were isolated…. 
Looks to me like trimethylglycine, an amino-acid derivative found in plants…

Regards,

Jeroen
__
https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

Dear All,

I am a first-year PhD student in a structural biology lab. I am building a 
model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions 
for fitting a ligand in an unknown X-ray density (attached image) in the 
protein binding pocket. The details for protein purification and 
crystallization buffers are below:

Purification: NaCl, Tris-HCl pH 8.5, Glycerol
Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium 
citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, 
Precipitant (PEG3350, MPD)

I have tried fitting all the buffer and crystallization components but none of 
these components are giving the right solution (Either the difference map gets 
red with increased B-factor or it remains green).
I would really appreciate your input on this. I have attached an image showing 
the density.

Thank you.





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Re: [ccp4bb] Ligand identification in X-ray density

[Jon Cooper]

Or, it could be MPD ;-?

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android

 Original Message 
On 05/06/2024 17:54, Jeroen Mesters wrote:

> Thank you for this intriguing information!
>
> At the same time, this also implies that not all entities that have been 
> modelled as MPD are actually MDP but could also be a betain, right!?…..
>
> Best,
>
> Jeroen
>
> __
> Dr. math. et dis. nat. Jeroen R. Mesters
> Biological Safety Officer (BBS)
> Deputy, Lecturer, Program Coordinator Infection Biology
> Visiting Professorship in Biophysics South Bohemian University
> University of Lübeck
> Center for Structural and Cell Biology in Medicine
> Institute of Biochemistry
> Ratzeburger Allee 160
> 23562 Lübeck
>
> https://orcid.org/-0001-8532-6699
>
>> Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :
>>
>> Hello Everyone,
>>
>> It does look like trimethylglycine (betaine), but another view might help. 
>> If it is, it is also made in ecoli and PEOPLE. It is a pretty common 
>> metabolite in the microbial and animal kingdom…useful for balancing osmotic 
>> stress and stabilizing protein structure (it is a strong kosmotrope).
>>
>> Best regards,
>>
>> Z
>>
>> ***
>> Zachary A. Wood, Ph.D. (He/Him)
>> Professor and Graduate Coordinator
>>
>> Josiah Meigs Distinguished Teaching Professor
>>
>> Associate Director of SER-CAT
>> Department of Biochemistry & Molecular Biology
>> University of Georgia
>> Life Sciences Building, Rm A426B
>> 120 Green Street
>> Athens, GA 30602-7229
>> Office: 706-583-0304
>> Lab: 706-583-0303
>> FAX: 706-542-1738
>> ***
>>
>> From:CCP4 bulletin board  on behalf of Jeroen Mesters 
>> 
>> Date:Wednesday, June 5, 2024 at 12:29 PM
>> To:CCP4BB@JISCMAIL.AC.UK
>> Subject:Re: [ccp4bb] Ligand identification in X-ray density
>>
>> You don't often get email 
>> fromcf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk.[Learn why this is 
>> important](https://aka.ms/LearnAboutSenderIdentification)
>>
>> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>>
>> Hi,
>>
>> proteins my pick up ligands from the „source" from which they were 
>> isolated…. Looks to me like trimethylglycine, an amino-acid derivative found 
>> in plants…
>>
>> Regards,
>>
>> Jeroen
>>
>> __
>>
>> https://orcid.org/-0001-8532-6699
>>
>>> Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
>>> :
>>>
>>> Dear All,
>>>
>>> I am a first-year PhD student in a structural biology lab. I am building a 
>>> model in 1.5 ang X-ray diffraction data. I would appreciate your 
>>> suggestions for fitting a ligand in an unknown X-ray density (attached 
>>> image) in the protein binding pocket. The details for protein purification 
>>> and crystallization buffers are below:
>>>
>>> Purification: NaCl, Tris-HCl pH 8.5, Glycerol
>>>
>>> Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, 
>>> Sodium citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine 
>>> buffer, Precipitant (PEG3350, MPD)
>>>
>>> I have tried fitting all the buffer and crystallization components but none 
>>> of these components are giving the right solution (Either the difference 
>>> map gets red with increased B-factor or it remains green).
>>>
>>> I would really appreciate your input on this. I have attached an image 
>>> showing the density.
>>>
>>> Thank you.
>>
>> ---
>>
>> 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] Ligand identification in X-ray density

[Jeroen Mesters]

Thank you for this intriguing information!

At the same time, this also implies that not all entities that have been 
modelled as MPD are actually MDP but could also be a betain, right!?…..

Best,

Jeroen
__
Dr. math. et dis. nat. Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics South Bohemian University
University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 18:41 schrieb Zachary A. Wood :

Hello Everyone,

It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Ligand identification in X-ray density

You don't often get email from 
cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk<mailto:cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>.
 Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi,

proteins my pick up ligands from the „source" from which they were isolated…. 
Looks to me like trimethylglycine, an amino-acid derivative found in plants…

Regards,

Jeroen
__
https://orcid.org/-0001-8532-6699


Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

Dear All,

I am a first-year PhD student in a structural biology lab. I am building a 
model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions 
for fitting a ligand in an unknown X-ray density (attached image) in the 
protein binding pocket. The details for protein purification and 
crystallization buffers are below:

Purification: NaCl, Tris-HCl pH 8.5, Glycerol
Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium 
citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, 
Precipitant (PEG3350, MPD)

I have tried fitting all the buffer and crystallization components but none of 
these components are giving the right solution (Either the difference map gets 
red with increased B-factor or it remains green).
I would really appreciate your input on this. I have attached an image showing 
the density.

Thank you.





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] Ligand identification in X-ray density

[David J. Schuller]

"but another view might help."

I second that. I would specifically like to be assured that it is not sitting 
on a special symmetry position.

===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
 schul...@cornell.edu

From: CCP4 bulletin board  on behalf of Zachary A. Wood 
<d585377c7e8a-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, June 5, 2024 12:41 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ligand identification in X-ray density


Hello Everyone,



It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).



Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator

Josiah Meigs Distinguished Teaching Professor

Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***





From: CCP4 bulletin board  on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ligand identification in X-ray density

You don't often get email from cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hi,



proteins my pick up ligands from the „source" from which they were isolated…. 
Looks to me like trimethylglycine, an amino-acid derivative found in plants…



Regards,



Jeroen

__

https://orcid.org/-0001-8532-6699



Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:



Dear All,



I am a first-year PhD student in a structural biology lab. I am building a 
model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions 
for fitting a ligand in an unknown X-ray density (attached image) in the 
protein binding pocket. The details for protein purification and 
crystallization buffers are below:



Purification: NaCl, Tris-HCl pH 8.5, Glycerol

Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium 
citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, 
Precipitant (PEG3350, MPD)


I have tried fitting all the buffer and crystallization components but none of 
these components are giving the right solution (Either the difference map gets 
red with increased B-factor or it remains green).

I would really appreciate your input on this. I have attached an image showing 
the density.



Thank you.









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] Ligand identification in X-ray density

[Zachary A. Wood]

Hello Everyone,

It does look like trimethylglycine (betaine), but another view might help. If 
it is, it is also made in ecoli and PEOPLE. It is a pretty common metabolite in 
the microbial and animal kingdom…useful for balancing osmotic stress and 
stabilizing protein structure (it is a strong kosmotrope).

Best regards,

Z


***
Zachary A. Wood, Ph.D. (He/Him)
Professor and Graduate Coordinator
Josiah Meigs Distinguished Teaching Professor
Associate Director of SER-CAT
Department of Biochemistry & Molecular Biology
University of Georgia
Life Sciences Building, Rm A426B
120 Green Street
Athens, GA  30602-7229
Office: 706-583-0304
Lab:706-583-0303
FAX: 706-542-1738
***


From: CCP4 bulletin board  on behalf of Jeroen Mesters 
<cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk>
Date: Wednesday, June 5, 2024 at 12:29 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Ligand identification in X-ray density
You don't often get email from cf8d8aa45b08-dmarc-requ...@jiscmail.ac.uk. 
Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>
[EXTERNAL SENDER - PROCEED CAUTIOUSLY]
Hi,

proteins my pick up ligands from the „source" from which they were isolated…. 
Looks to me like trimethylglycine, an amino-acid derivative found in plants…

Regards,

Jeroen
__
https://orcid.org/-0001-8532-6699


Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

Dear All,

I am a first-year PhD student in a structural biology lab. I am building a 
model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions 
for fitting a ligand in an unknown X-ray density (attached image) in the 
protein binding pocket. The details for protein purification and 
crystallization buffers are below:

Purification: NaCl, Tris-HCl pH 8.5, Glycerol
Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium 
citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, 
Precipitant (PEG3350, MPD)

I have tried fitting all the buffer and crystallization components but none of 
these components are giving the right solution (Either the difference map gets 
red with increased B-factor or it remains green).
I would really appreciate your input on this. I have attached an image showing 
the density.

Thank you.





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] Ligand identification in X-ray density

[Jeroen Mesters]

Hi,

proteins my pick up ligands from the „source" from which they were isolated…. 
Looks to me like trimethylglycine, an amino-acid derivative found in plants…

Regards,

Jeroen
__
https://orcid.org/-0001-8532-6699

Am 05.06.2024 um 17:44 schrieb Khadijah Ameen Khan 
:

Dear All,

I am a first-year PhD student in a structural biology lab. I am building a 
model in 1.5 ang X-ray diffraction data. I would appreciate your suggestions 
for fitting a ligand in an unknown X-ray density (attached image) in the 
protein binding pocket. The details for protein purification and 
crystallization buffers are below:

Purification: NaCl, Tris-HCl pH 8.5, Glycerol
Crystallization: Carboxylic acid mix (Sodium formate, Ammonium acetate, Sodium 
citrate, Potassium Sodium Tartrate and Sodium Oxamate),Tris, Bicine buffer, 
Precipitant (PEG3350, MPD)

I have tried fitting all the buffer and crystallization components but none of 
these components are giving the right solution (Either the difference map gets 
red with increased B-factor or it remains green).
I would really appreciate your input on this. I have attached an image showing 
the density.

Thank you.





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] Resampling CryoEM Density map to XRD Density map for Difference Map

[Paul Emsley]

On 05/06/2024 07:00, Devbrat Kumar wrote:



--

Hello Everyone,


Hello Devbrat,


I have a query regarding the resampling of cryoEM density to match 
crystal density to obtain a density difference map. Specifically, I am 
trying to determine if it is feasible to resample a cryoEM map with an 
XRD density map. However, each time I attempt this, the resampling 
output provides an arbitrary ASU resample map, resulting in a 
significant loss of major density.


I have been using Coot and Chimera for this process but have not 
achieved the desired outcome. Please guide me or suggest how to move 
forward with this. My goal is to create an accurate final density 
difference map.





It is not clear to me exactly what the problem is.

In Coot speak, "resampling" is (merely) changing the grid sampling so 
that the map appears (typically) on a finer grid.


I don't think that this is what you want.

You want is, I think, "Transform Map by LSQ Model-fit" and if that is 
what you used, then I can't help until I am more clear about what you 
think has gone wrong.


Regards,

Paul.




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Re: [ccp4bb] E. coli strain M15 or SG13009 - muchas gracias to all who replied

[Mark J. van Raaij]

Many thanks to all who took out some time to reply.

Summary:

you can also use
https://www.neb.com/en/products/c3037-nebexpress-iq-competent-e-coli-high-efficiency
 this has LacIq, we use it with all our pQE bassed vectors.

Gentauer may still sell those…
https://maxanim.com/strains/m15-prep4-escherichia-coli-strains/

we have just today obtained a plate with M15(pREP4) from someone at another lab 
in Madrid who also subscribes to ccp4bb.

other people also offered the pREF4 plasmid



Mark van Raaij
Dpto de Estructura de Macromoleculas, lab 20B
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. +34 91 585 4616 (internal 432092)


> 
> 
>> Am 31.05.2024 um 13:17 schrieb Mark J. van Raaij :
>> 
>> Dear All.
>> 
>> we are looking for E. coli strain M15 or SG13009 to use for expressing a 
>> protein from the vector pQE30. Are these strains still availabe commercially?
>> If not, we'd be open for another way to obtain an aliquot.
>> 
>> Wbw,
>> 
>> Mark
>> 
>> 
>> Mark van Raaij
>> Dpto de Estructura de Macromoleculas, lab 20B
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> E-28049 Madrid, Spain
>> tel. +34 91 585 4616 (internal 432092)
>> 
>> 
>> 
>> 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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