[ccp4bb] postdoc position available

[Chang, Changsoo]

Argonne National Laboratory seeks a postdoctoral researcher to join the 
Structural Biology Center (SBC) at the Advanced Photon Source (APS) to develop 
methods in crystallography and other techniques. Building on our expertise in 
high resolution de novo structure determination, serial crystallography and a 
long history of cutting edge experiments, we would like to bring the next 
generation of experiments to the SBC general user program. The postdoctoral 
fellow will develop hardware and software to analyze molecular changes of 
structures as diffraction data is collected and processed autonomously, will 
create the experimental scope, source samples, collect and analyze data.

The SBC is committed to research in these areas as the direction of the 
crystallography is being shifted and as APS will provide advanced capabilities 
after the major ongoing upgrade. Research in multimodal crystallography is 
growing and expected to continue to increase for years to come.


Please see link.

https://careers.peopleclick.com/careerscp/client_argonnelab/post_doc/gateway.do?functionName=viewFromLink=7771=en-us


Changsoo Chang






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Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

[Edward A. Berry]

On 05/19/2019 08:21 AM, Ian Tickle wrote:
~~~

So there you have it: what matters is that the _errors_ in the NCS-related 
amplitudes are uncorrelated, or at least no more correlated than the errors in 
the non-NCS-related amplitudes, NOT the amplitudes themselves.


Thanks, Ian!

I would like to think that it is the errors in Fobs that matter (as may be the 
case), because then:
1. ncs would not bias R-free even if you _do_ use ncs constraints/restraints. 
(changes in Fcalc due to a step of refinement would be positively correlated 
between sym-mates, but if the sign of (Fo-Fc) is opposite at the sym-mate, what 
impoves the working reflection would worsen the free)
2. There would be no need to use the same free set when you refine the 
structure against a new dataset (as for ligand studies) since the random errors 
of measurement in Fobs in the two sets would be unrelated.

However when I suggested that in a previous post, I was reminded that errors in Fobs 
account for only a small part of the difference (Fo-Fc). The remainder must be due to 
inability of our simple atomic models to represent the actual electron density, or its 
diffraction; and for a symmetric structure and a symmetric model, that difference is 
likely to be symmetric.  Whether that difference represents "noise" that we 
want to avoid fitting is another question, but it is likely that (Fo-Fc) will be 
correlated with sym-mates. So I settled for convincing myself that the changes in Fc 
brought about by refinement would be uncorrelated, and thus the _changes_ in (Fo-Fc) at 
each step would be uncorrelated.

Below are some of the ideas I come up with in trying to think about this, and 
about bias in general. (Not very well organized and not the best of prose, but 
if one is a glutton for punishment, or just wants to see how the mind of a 
madman works . . .)

Warning- some of this is contrary to current consensus opinion and the 
conclusions may be, in the words of a popular autobuilding program, partly 
WRONG!  In particular, the idea that coupling by the G-function does not bias 
R-free, but rather is the only reason that R-free works at all!
- - - - - - - - - -

The differences (Fo-Fc) can be divided between (1) errors in measurement
of reflection intensities and (2)failure of the model to represent the
true structure. The first can be considered "noise" and we would expect
it to be random, with no correlation between symm mates.
However most of the difference between Fc and Fobs is not due to random
noise in the data, but to failures of our model to accurately represent
the real thing. These differences are likely to be ncs-symmetric.
Leaving aside the question of whether or not we want to fit this kind of
"noise" (bringing the model closer to the real structure?), we conclude
that (Fo-Fc) is likely to be correlated between ncs-mates.

But for refinement against the working set to bias the contribution of
sym-related free-set reflections to R-free would require that _changes_
in |Fo-Fc| from a step of refinement would be ncs-correlated. If on the
contrary they are not correlated, i.e. if a change that decreases
|Fo-Fc| for a working reflection is equally likely to decrease or
increase |Fo-Fc| for its sym mate (which may be) in the free set, then
it is hard to see how refinement against the working reflection would
bias R-free.

Under what conditins would |Fo-Fc| for symmetry related reflections be
correlated? This would be the case if change in Fc correlates AND the
sign of (Fo-Fc) correlates. Again, if the difference were only due to
random error in Fobs, then the sign of Fo-Fc of a symmetry related reflection
would be as likely to be the opposite as the same (as the original
reflection) so even if changes in Fc are correlated, what improves the
fit to the original reflection would be as likely to worsen the fit to
its mate. But we concluded above that Fo-Fc is likely to be correlated
by symmetry, since the shortcomings of our model are likely to be
symmetric. So we ask if changes in Fc are correlated.

So why should a structural change result in correlated changes of
symm-related Fc's?
The Fc is the amplitude of the best-fit sin wave (of the specified
frequency) to the projection of the density of the crystal onto the
specified scattering vector. The refinement program can increase Fcalc
by moving an atom so that its projection on the scattering vector moves
toward a peak of that sine wave, or decrease it by moving away from a peak.
If the projection of an atom on the scattering vector moves toward a
peak, the density becomes more peaked and the amplitude increases, if it
moves toward a trough it tends to take density away from the peak or
fill in the trough and the density becomes flatter.

But the scattering vector of a sym-related reflection is at a different
angle, anywhere from almost 0 to 90 degrees from its mate (actually to
180*, but then the Friedel mate is close to zero- Its a question of how
parallel they are, 

Re: [ccp4bb] tNCS incompatible with cell dimensions

[Kevin Jude]

Thanks everybody for your replies. I am having another look at my data in
P1 and will post an update and summary to the list.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431


On Fri, May 31, 2019 at 1:09 PM Kevin Jude  wrote:

> Hello community, I wonder if I could solicit advice about a problematic
> dataset. I plan to solve the structure by molecular replacement and expect
> that the protein is relatively compact, ie not elongated. SAXS data
> supports this expectation.
>
> The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2
> with a = 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with
> 40% solvent. The native Patterson shows a large peak (12 sigma) suggesting
> a tNCS vector of {0.5, 0.5, 0}.
>
> If you're sharper than me, you may have already spotted the problem - c is
> the long axis of the unit cell, but tNCS constrains the proteins to a plane
> parallel to the a,b plane. Indeed, molecular replacement attempts using
> Phaser will not give a solution in any orthorhombic space group unless I
> turn off packing, and then I get large overlaps in the a,b plane and huge
> gaps along c.
>
> Since I believe that my model is good (or at least the correct shape,
> based on SAXS), I wonder if I'm misinterpreting my crystallographic data.
> Any insights into how to approach this problem would be much appreciated.
>
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
>



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Re: [ccp4bb] 40th CCP4 anniversary competition - 10 Golden Tickets deadline 18th June!

[Andreas Förster]

Would it be fair to call it CCP40 now?


Andreas



On Mon, Jun 3, 2019 at 4:37 PM Paula Salgado 
wrote:

>
>
> This year, CCP4 turns 40 and is celebrating in style with an event in
> London. CCP4 has a strong focus on training the new generation of
> crystallographers and developers so, as part of the celebrations, we are
> inviting 10 PhD students and Post-doctoral researchers to showcase their
> work using CCP4.
>
>
>
> If you are a PhD student or Postdoc protein crystallographer and have
> published work featureing CCP4 as a strong component, or have made a
> recognised contribution to CCP4 software, you could be joining the
> celebrations at the Royal Society, London, on *Tuesday 9 July, from
> 13:00-17:00*.
>
>
>
> To win, just submit a piece of published work highlighting CCP4, where you
> are the first author. If selected, you will be asked to create a poster to
> present to a wide range of audiences at the event.  Small travel
> bursaries are available to help with costs (details
> http://www.ccp4.ac.uk/40thccp4golden.htm).
>
>
> Deadline to apply is *June 18th,* so hurry! Please share with your
> students, postdocs, colleagues and friends! We want to hear about your
> great work and want you to join the party on July 9th!
>
>
> Attached is a flyer you can use to help advertise the competition.
>
>
> Hope to see you at the Royal Society!
>
>
> Competition details :
>
> http://www.ccp4.ac.uk/40thccp4golden.htm
>
>
>
> On behalf of the CCP4 Executive
>
> Paula Salgado
>
>
> ===
>
> Dr Paula S. Salgado
> Senior Lecturer in Macromolecular Crystallography
> Institute for Cell and Molecular Biosciences
> Faculty of Medical Sciences
> 3rd Floor Cookson Building
> Newcastle University
> Newcastle upon Tyne, NE2 4HH, UK
>
> Tel: +44 (0)191 208 7432
> Fax: +44 (0)191 208 7424
> Email: paula.salg...@ncl.ac.uk
>
> --
>
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> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

[dusan turk]

Dear Jonathan,

Here is some additional explanation on the NCS dependent and NCS independent 
R-free issues.

I think that we all agree that redundancy is related to the accuracy of a 
measurement. The higher redundancy a data set has, the more accurate its 
average value is. In crystallography, if we have a P1 P6 space groups. We can 
also agree that it is clear if we collect and process data set rotated about an 
arbitrary spindle axes for 180 degrees, then the data of the P6 space group 
will have approximately 6-times higher redundancy then the P1 when merged to 
the asymmetric unit. However, the asymmetric unit of P6 is 6-times smaller than 
of P1. If we leave out a small portion of data from the P6 data set, it will 
not really effect completeness, even the processed data will be almost the same 
and similar it will be true for the P1 data set. The difference will be only in 
redundancy and thereby accuracy. However if we leave out 5/6 also considering 
the Friedel symmetry, then the P6 data set will still have high completeness, 
whereas the P1 data set will be highly incomplete. The same argument can be 
applied for data with NCS as demonstrated by the Silva and Rossmann paper. 
Hence, one can remove a lot of data from a system with high NCS, and the system 
will still be completely described, even though the lowered redundancy will 
lower the accuracy. What I want to say is that redundancy is good, it increases 
accuracy, whereas to the bias of NCS in R-free, the NCS bias is there and 
therefore understandable that the Rfree gap should remain the same as well as 
R-work and R-free. I am actually surprised that they are that different.

On the R-work, R-free and R-free gap of the molecules without NCS, the visual 
comparison of numbers does not provide a validated answer on whether they 
correspond to the same structure or not.  This is a matter of the accuracy of 
requirements. As it is appears from your message, your requirements were met, 
hence you are right. However, to answer the question whether the differences 
between them are meaningful (are the structures equally apart from the true 
answer) one must not only look at R-work and R-frees, but also into the 
accompanying model that delivers these numbers. In order to deliver a validated 
statement about the relationship between R-free gap and the structure 
correctness one needs a references (the actual objects) to which these refined 
structures are compared to. In our paper we used two comparisons: RMSD 
deviations between the refined and the true reference structure, and average 
phase difference between Fcalc of the refined model and those of the true 
reference structure. Because in reality we do not have the true true 
structures, for our analysis to be valid we have chosen data sets with 
truncated high resolution, a model with errors, and starting models (coming out 
of molecular replacement) and compared them with the final structures. All 
these tests were based on the assumption that when the target model is far 
enough from the starting point, then the final refined structure can be used as 
the reference of the true true structure. To deliver a validated statement 
about the poor to nonexistent correlation between the R-free gap and phase 
error of the model we selected 31 different data sets with different portions 
of the TEST set and refined each structure against each of the set until 
convergence without including any model rebuilding and human intervention. And 
then we calculated their “correlation” between the phase errors and R-free gap 
and established that the relation is poor or nonexistent. So, in the absence of 
the comparison with the true reference structures, it is in my opinion 
impossible to establish whether the differences between the numbers in the 
table you calculated are meaningful or not.

I hope this helps,

dusan


> On 3 Jun 2019, at 01:00, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Sun, 2 Jun 2019 19:28:04 +0100
> From:Eleanor Dodson 
> Subject: Re: Does ncs bias R-free? And if so, can it be avoided by special 
> selection of the free set?
> 
> The current Rfree selection is done in the highest possible Laue group - eg
> trigonal uses P6/mmm - then the selection is proogated to the chosen Laue
> group - eg P3. So IF the ncs reflects a higher Laue symmetry as it often
> does the FreeR is sort of buffered against the ncs- effect..
> 
> That wont always be true of course but it does help avoid NCS bias.
> Eleanor
> 
> On Sat, 1 Jun 2019 at 22:57, Jonathan Cooper <
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
>> I have done some more tests with different programs for choosing the
>> R-free set in shells or at random and the results are at the same link:
>> 
>> https://www.ucl.ac.uk/~rmhajc0/rfreetests.pdf
>> 
>> There still seems to be no significant difference between the normal
>> R-free and the R-free in shells, with up to 20-fold NCS present. I can't
>> comment on 

[ccp4bb] Postdoc Opening - Multi-Dataset Crystallography and Allostery - Keedy Lab, New York City

[Daniel Keedy]

The Daniel Keedy Lab at the CUNY Advanced Science Research Center in New York 
City has an available position for a Postdoctoral Researcher starting 
immediately.

The Keedy Lab aims to elucidate the conformational ensembles of proteins and to 
understand how they are shifted by perturbations, including mutations, 
protein:protein interactions, and ligands, to control function.  We are 
especially interested in how “hidden” conformational ensembles drive 
differences in allosteric regulatory mechanisms for protein tyrosine 
phosphatases (PTPs), which are under-studied but biologically critical.  To 
explore these questions, we are developing new multi-dataset approaches in 
X-ray crystallography that couple advances in automated data collection and 
multi-state modeling algorithms.  For more information, visit our newly 
designed lab website: www.keedylab.org

The ideal applicant should have a strong background in macromolecular X-ray 
crystallography, whether experimental, computational, or both.  Experience 
writing or contributing to scientific software is also preferred.  Candidates 
with other expertise in biophysics, computational biology, or related areas are 
also welcome to apply.

The CUNY Advanced Science Research Center is a new cutting-edge research 
institution located in upper Manhattan in New York City -- the "greatest city 
in the world".  The Structural Biology Initiative of the ASRC features seven 
tenure-track and research-track faculty members, pursuing diverse research 
problems using X-ray diffraction, cryo-EM, NMR, mass spectrometry, solution 
biophysics, and advanced microscopy.  The ASRC is immediately adjacent to the 
New York Structural Biology Center, a consortium of CUNY and eight other New 
York academic institutions with world-class facilities, and 70 miles from 
Brookhaven National Laboratory, featuring the newly constructed National 
Synchrotron Light Source II, now the brightest synchrotron light source in the 
United States.  The ASRC will also enjoy use of a new dedicated 
high-performance computing cluster starting this fall.

You can officially apply for the position here:

https://cuny.jobs/new-york-ny/research-associate-structural-biology-initiative/3F61F1DE234B4BF7BA9E5777089B982C/job/

Feel free to contact Dr. Keedy directly at 
daniel.ke...@asrc.cuny.edu with your CV and 
a brief description of your interests if you would like to discuss possible 
projects.

Please pass this ad along to others who may be interested.

Come join us in NYC!

~Daniel Keedy

—
Daniel A. Keedy, Ph.D.
Assistant Professor
Structural Biology Initiative, CUNY Advanced Science Research Center
Department of Chemistry and Biochemistry, City College of New York
Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center
www.keedylab.org   |  
daniel.ke...@asrc.cuny.edu  |  212-413-3246




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[ccp4bb] On behalf Abbas Ourmazd: Machine-learning Opportunities

[Schertler Gebhard (PSI)]

Abbas Ourmazed has developed interesting data analysis approaches to XFEL and 
Cryo-EM data they apply simmilar strategies to other typs of data.



Machine-learning Opportunities at the University of Wisconsin Milwaukee

The Data Science/Machine Learning group in the Department of Physics plans to 
hire up to three postdoctoral associates in applications of machine learning to 
physics and biology.

We seek outstanding candidates to pioneer the development and application of 
advanced machine learning techniques to key problems at the forefront of 
science. While familiarity with machine learning would be an advantage, 
exceptional candidates will receive serious consideration regardless of 
background.

Please send applications (cover letter, resume & publications list) to Prof. 
Abbas Ourmazd [ourm...@uwm.edu].







Prof. Gebhard F.X. Schertler
Structural Biology ETH Zürih D-BIOL

Head of Biology and Chemistry
Division
Paul Scherrer Institut
Laboratory of Biomolecular Research,
LBR
OFLC 109
CH-5232 Villigen PSI
gebhard.schert...@psi.ch
phone +41 56 310 4265






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Re: [ccp4bb] PyMOL now packaged as a snap on Linux

[Pedro Matias]

Well, I can't get it to work in FC30 - I installed FC30 on a virtual
machine and managed to install both snapd and pymol-oss but pymol does
not run as a command.

Am I missing something rather obvious?

Pedro

Às 12:46 de 03/06/2019, Matic Kisovec escreveu:
> Hi,
>
> thank you very much for this. Work fine on Ubuntu 19.04.
>
> Kind regrds,
> Matic
>
>
> On 17. 05. 19 20:04, Arunabh Athreya wrote:
>> Thanks for sharing this.
>>
>> Get Outlook for Android 
>>
>> 
>> *From:* CCP4 bulletin board  on behalf of
>> David Schuller 
>> *Sent:* Thursday, May 16, 2019 11:41:19 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] PyMOL now packaged as a snap on Linux
>>  
>> It seems to work on Fedora 30 and on Scientific Linux 7 (which means
>> it should also work on RHEL7 and Centos 7)
>>
>> Thank you.
>>
>>
>>
>> On 5/16/19 10:47 AM, Darren Hart wrote:
>>> Some more info:
>>>
>>> https://snapcraft.io/pymol-oss
>>>
>>> It seems to work exactly as expected.
>>>
>>> Darren
>>>
>>>
>>> On 16/05/2019 16:05, Folmer Fredslund wrote:
 Hi Darren,

 That's brilliant!

 I'll give it a spin and see how it works. 

 Best regards
 Folmer 


 tor. 16. maj 2019 13.02 skrev Darren Hart >>> >:

 Since yesterday, PyMOL (open source version v2.3) has been
 packaged as a
 distro-independent "snap" that can be installed easily on linux
 platforms - no more cloning from gitlab and compiling after
 installing
 the dependencies.

 On Ubuntu, install from software centre or:

 sudo snap install pymol-oss

 Many distros have the snap architecture already installed. If
 not, you
 just need to install snapd in the regular way first (e.g. on
 Debian:
 sudo apt install snapd).

 Hope this is useful for some folks.

 Best regards,

 Darren

 
 

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

>>>
>>> -- 
>>>
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
>> -- 
>> ===
>> All Things Serve the Beam
>> ===
>>David J. Schuller
>>modern man in a post-modern world
>>MacCHESS, Cornell University
>>schul...@cornell.edu
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> 
>
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>
-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8




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[ccp4bb] Fwd: [ccp4bb] AKTA FPLC fractionation peak by peak

[Sorin Draga]

Thank you both for your answers!

*Upasana* - the chromatogram was randomly selected to ilustrate the point -
we do a careful equilibration of the column and degas the mobile phase(s)
before starting. I'm not really sure what you mean by oligomeric state of
the protein - we are working with complex proteic mixtures that are not
characterized, hence the need for fractionation.
*Matthias* - your advice is spot on! I will give it a try and keep you
posted.


On Mon, Jun 3, 2019 at 10:24 AM Barone, Matthias 
wrote:

> Hi sorin
> The problem in your elution profile is that you cannot define a global
> threshold as the baseline is heavily bent (relative to the peak heights)
> and starting to fractionate at 6' is not the problem, telling the script to
> stop once you reach baseline at 13' is.
> I would try what you proposed: Given that your peak elution time points
> are reproducible, I'd actually work with the "watch" function and turn it
> on while watching OD for the given time windows.  fractionate the first
> block when OD exceeded a certain threshold and then turn the watch function
> off after, say 13'. Turn it back on at 20' and fractionate into another
> well. Use the time as base and keep the Äkta pumping at constant speed.
> Curious if someone knows a better strategy!
> Best, matthias
>
> --
> *From:* CCP4 bulletin board  on behalf of Sorin
> Draga 
> *Sent:* Monday, June 3, 2019 8:29:40 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] AKTA FPLC fractionation peak by peak
>
> Dear all,
>
> We have an old akta system, running Unicorn 4.0, recently donated to our
> lab. While attempting to fractionate a protein mixture, I was unable to
> convince Unicorn to fractionate within given limits (say, for ex peak A
> between RT a and b and peak B between retention times c and d). All that I
> could manage to do is fractionate at a fixed time interval.
> For clarity, I have attached a picture below (orange square would be what
> we actually want to fractionate)
> Any help would be appreciated, as we are pressed for time ( I am certain
> that we are missing something simple)
>
> Thank you!
> [image: image.png]
>
>
> --
>
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Re: [ccp4bb] PyMOL now packaged as a snap on Linux

[Matic Kisovec]

Hi,

thank you very much for this. Work fine on Ubuntu 19.04.

Kind regrds,
Matic


On 17. 05. 19 20:04, Arunabh Athreya wrote:
Thanks for sharing this.

Get Outlook for Android


From: CCP4 bulletin board  
on behalf of David Schuller 
Sent: Thursday, May 16, 2019 11:41:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PyMOL now packaged as a snap on Linux

It seems to work on Fedora 30 and on Scientific Linux 7 (which means it should 
also work on RHEL7 and Centos 7)

Thank you.



On 5/16/19 10:47 AM, Darren Hart wrote:
Some more info:

https://snapcraft.io/pymol-oss

It seems to work exactly as expected.

Darren


On 16/05/2019 16:05, Folmer Fredslund wrote:
Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart 
mailto:darren.h...@ibs.fr>>:
Since yesterday, PyMOL (open source version v2.3) has been packaged as a
distro-independent "snap" that can be installed easily on linux
platforms - no more cloning from gitlab and compiling after installing
the dependencies.

On Ubuntu, install from software centre or:

sudo snap install pymol-oss

Many distros have the snap architecture already installed. If not, you
just need to install snapd in the regular way first (e.g. on Debian:
sudo apt install snapd).

Hope this is useful for some folks.

Best regards,

Darren



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




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Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

[Ian Tickle]

Eleanor, what exactly is the mechanism whereby NCS leads to correlation of
measurement errors, and thereby could cause cross-validation bias?

As you know, the aim of cross-validation is to guard against overfitting,
where as a consequence over-parameterisation some or all of the structural
parameters are fitted to the errors in Fobs, resulting in the undesirable
propagation of those errors into the structure.  For the CV metric (Rfree
or better LLfree) to be unbiased any correlation between the errors in the
working set and the test set Fobs should be minimised, so that Fobs with
correlated errors should be kept together either in the working set or the
test set, but not split between them.  This is _not_ the same thing as
saying that correlated Fs should be kept together.

I'm having a hard time understanding how NCS leads to correlation of
measurement errors: please explain.  Of course there will be correlation
between measurement errors due for example to errors in the batch scale
factors (so the errors in all intensities on the same or adjacent images
will surely be correlated), but what does that have to do with NCS?  Errors
in scale factors will cause correlation between the errors of _all_
reflections on the same or adjacent images, not just the NCS-related ones.
Would you propose to keep all reflections from the same images together in
the working or test set to avoid the effect of this correlation of errors?

I suspect there is some confusion here between the correlation of the Fs
(which NCS certainly has some bearing on) and the correlation of the
_errors_ in the Fs which AFAICS has nothing to do with NCS.  For the
mitigation of cross-validation bias we are only concerned with reducing the
correlations of the errors in the Fs by appropriate selection of the test
set.  Also note that the error in F (= Fobs - Ftrue) is not the same as the
uncertainty in F (= sigma(F)).  NCS will surely cause correlation of
uncertainties, simply because the NCS-related Fs are correlated and
uncertainties are correlated with Fs, but AFAICS the magnitudes of the
uncertainties are as irrelevant here as the magnitudes of the Fs.

Cheers

-- Ian


On Sun, 2 Jun 2019 at 19:28, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> The current Rfree selection is done in the highest possible Laue group -
> eg trigonal uses P6/mmm - then the selection is proogated to the chosen
> Laue group - eg P3. So IF the ncs reflects a higher Laue symmetry as it
> often does the FreeR is sort of buffered against the ncs- effect..
>
> That wont always be true of course but it does help avoid NCS bias.
> Eleanor
>
> On Sat, 1 Jun 2019 at 22:57, Jonathan Cooper <
> 0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I have done some more tests with different programs for choosing the
>> R-free set in shells or at random and the results are at the same link:
>>
>> https://www.ucl.ac.uk/~rmhajc0/rfreetests.pdf
>>
>> There still seems to be no significant difference between the normal
>> R-free and the R-free in shells, with up to 20-fold NCS present. I can't
>> comment on twinning, but with NCS it would seem that the normal CCP4 way of
>> picking the R-free set is as good as anything else!
>> On Sunday, 26 May 2019, 14:02:50 BST, dusan turk 
>> wrote:
>>
>>
>> Dear colleagues,
>>
>>
>> > Does ncs bias R-free? And if so, can it be avoided by special selection
>> of
>> the free set?
>>
>> It occurs to me that we tend to forget that the objective of structure
>> determination is not the model with the lowest model bias, but the model
>> which is closest to the true structure. The structure without model bias is
>> the structure without a model - which is not really helpful.
>>
>> An angle on the NCS issue is provided by the work of Silva & Rossmann
>> (1985, Acta Cryst B41, 147-157), who discarded most of data almost
>> proportionally to the level of NCS redundancy (using 1/7th for WORK set and
>> 6/7 for TEST set in the case of 10-fold NCS). They did it in 1990s in order
>> to make refinement of their large structure computationally feasible:
>> “Despite the reduction in the number of variables imposed by the
>> non-crystallographic constraints, the problem remained a formidable one if
>> all 298615 crystallographically independent reflections were to be used in
>> the refinement. However, the reduction of size of the asymmetric unit in
>> real space should be equivalent to a corresponding reduction in reciprocal
>> space. Hence, one-tenth of refinement of the independent data might suffice
>> for refinement.” In conclusion they stated that “This is the first time
>> that the structure of a complete virus has been refined by a
>> reciprocal-space method.” To conclude, to select an independent data set to
>> refined against, one should take an n-th fraction of reflections from the
>> data set containing the n-fold NCS.
>>
>> Now on the bias of the concept of R-free itself. As we known, each term
>> in the Fourier 

[ccp4bb] AW: [EXTERNAL] [ccp4bb] tNCS incompatible with cell dimensions

[Herman . Schreuder]

Dear Kevin,

It could also be that you have a particular nasty combination of tNCS and 
twinning. Given your packing problems in the ab plane, this would mean that 
your 2-fold parallel to c is generated by twinning and that probably one of the 
21 axes is generated by twinning as well.

With some very clever thinking, you might be able to figure out what the 
appropriate lower-symmetry space group would be, but I would follow the advice 
of John Helliwell: reprocess the data in P1 and run molecular replacement in 
P1. MR is usually quite insensitive to twinning and will produce two solutions 
with equal probability. Once you have the packing, you can try to figure out 
how to best describe this packing in terms of a space group with tNCS. If your 
data collection statistics do not suggest any twinning, you may have some other 
pathology like statistical disorder.

In any case, with this space group problem, you have great opportunity to learn 
a lot about crystallography!

Best,
Herman




Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Kevin 
Jude
Gesendet: Freitag, 31. Mai 2019 22:09
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] tNCS incompatible with cell dimensions


EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk

Hello community, I wonder if I could solicit advice about a problematic 
dataset. I plan to solve the structure by molecular replacement and expect that 
the protein is relatively compact, ie not elongated. SAXS data supports this 
expectation.

The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2 with a 
= 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with 40% 
solvent. The native Patterson shows a large peak (12 sigma) suggesting a tNCS 
vector of {0.5, 0.5, 0}.

If you're sharper than me, you may have already spotted the problem - c is the 
long axis of the unit cell, but tNCS constrains the proteins to a plane 
parallel to the a,b plane. Indeed, molecular replacement attempts using Phaser 
will not give a solution in any orthorhombic space group unless I turn off 
packing, and then I get large overlaps in the a,b plane and huge gaps along c.

Since I believe that my model is good (or at least the correct shape, based on 
SAXS), I wonder if I'm misinterpreting my crystallographic data. Any insights 
into how to approach this problem would be much appreciated.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431




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[ccp4bb] Fwd: Domainex is hiring a Structural Biologist

[Mark Roe]

Posted on behalf of Domainex.




Begin forwarded message:

From: Stefanie Reich mailto:s.re...@domainex.co.uk>>
Date: 31. May 2019 at 17:04:20 CEST
To: "ccp4bb@jiscmail.ac.uk" 
mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Domainex is hiring a Structural Biologist


https://www.domainex.co.uk/about-us/recruitment#3

  *



Domainex has a full-time permanent vacancy in our Protein Science Team, which 
offers our clients a comprehensive range of services including molecular 
biology, protein production for assays and structural biology, and structural 
analysis of proteins by X-ray crystallography.  Our unique, patented, 
Combinatorial Domain Hunting technology allows us to make and work with 
proteins that are otherwise refractory to recombinant expression.

All applicants must be able to solve X-ray crystal structures independently and 
have a good working knowledge of the current software packages employed in 
protein crystallography (esp. XDS, CCP4, coot). They should be able to 
demonstrate postdoctoral level experience of solving structures of 
protein-ligand complexes over a range of target classes in a drug discovery 
environment, experience in the use of biophysical techniques would be a 
significant plus. Candidates must also have expertise in molecular biology; 
recombinant protein expression and purification in E. coli, insect or mammalian 
cells; and substantial experience of using AKTA chromatography equipment (or 
similar) for protein purification to X-ray crystallography standard.

This role requires the ability to plan and implement experimental programmes, 
to solve any problems that arise, and to work effectively within project teams 
to deliver high-quality results to our clients. Laboratory work is a major 
element of this varied and challenging role.  Essential attributes include 
diligent reporting of results, data interpretation, and an ability to make 
recommendations for further studies. It will also be necessary to communicate 
your results effectively to our clients.



Job requirements:

PhD with track-record of relevant and proven experience, i.e. publications and 
PDB depositions.

Independence and team working; flexibility to take on different projects; 
ability to make a meaningful impact on clients.

Ability to work on your own initiative, and to consistently deliver high 
quality results.

Creative thinking coupled to delivery of novel outcomes that leads to 
opportunities for inventorship or publications (papers/research articles).



To apply for this role, please send your CV and a covering letter, quoting 
reference PS0519, to 
recruitment2...@domainex.co.uk.







Email confidentiality notice: This message is private and confidential. If you 
have received this message in error, please notify us and remove it from your 
system. Domainex Ltd is registered in England and Wales. Company No. 04336899. 
Registered office: Chesterford Research Park, Little Chesterford, Saffron 
Walden, Essex, CB10 1XL, UK.




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Re: [ccp4bb] AKTA FPLC fractionation peak by peak

[Barone, Matthias]

Hi sorin
The problem in your elution profile is that you cannot define a global 
threshold as the baseline is heavily bent (relative to the peak heights) and 
starting to fractionate at 6' is not the problem, telling the script to stop 
once you reach baseline at 13' is.
I would try what you proposed: Given that your peak elution time points are 
reproducible, I'd actually work with the "watch" function and turn it on while 
watching OD for the given time windows.  fractionate the first block when OD 
exceeded a certain threshold and then turn the watch function off after, say 
13'. Turn it back on at 20' and fractionate into another well. Use the time as 
base and keep the Äkta pumping at constant speed.
Curious if someone knows a better strategy!
Best, matthias


From: CCP4 bulletin board  on behalf of Sorin Draga 

Sent: Monday, June 3, 2019 8:29:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AKTA FPLC fractionation peak by peak

Dear all,

We have an old akta system, running Unicorn 4.0, recently donated to our lab. 
While attempting to fractionate a protein mixture, I was unable to convince 
Unicorn to fractionate within given limits (say, for ex peak A between RT a and 
b and peak B between retention times c and d). All that I could manage to do is 
fractionate at a fixed time interval.
For clarity, I have attached a picture below (orange square would be what we 
actually want to fractionate)
Any help would be appreciated, as we are pressed for time ( I am certain that 
we are missing something simple)

Thank you!
[image.png]




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[ccp4bb] AKTA FPLC fractionation peak by peak

[Sorin Draga]

Dear all,

We have an old akta system, running Unicorn 4.0, recently donated to our
lab. While attempting to fractionate a protein mixture, I was unable to
convince Unicorn to fractionate within given limits (say, for ex peak A
between RT a and b and peak B between retention times c and d). All that I
could manage to do is fractionate at a fixed time interval.
For clarity, I have attached a picture below (orange square would be what
we actually want to fractionate)
Any help would be appreciated, as we are pressed for time ( I am certain
that we are missing something simple)

Thank you!
[image: image.png]



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