Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

[Murpholino Peligro]

That's exactly what I am doing...
citing David...

"I expect the A and B data sets to be quite similar, but I would like to
evaluate which protocol was "better", and I want to do this quickly,
ideally looking at a single number."

and

"I do want to find a way to assess the various tweaks I can try in data
processing for a single case"

Why not do all those things with Rwork?
I thought that comparing the R-free rather than the R-work was going to be
easier Because last week the structure was dehydrated So the
refinement program added "strong waters" and due to a thousand or so extra
reflections I could have a dozen or so extra waters and the difference in
R-work value between protocols due to extra waters was going to be a little
bit more difficult to compare. I have now the final structure so I could
very well compare the R-work doing another round of refinement, maybe
randomizing adps at the beginning or something.

Thanks a lot.









El lun, 1 de nov. de 2021 a la(s) 03:22, David Waterman (
dgwater...@gmail.com) escribió:

> Hi James,
>
> What you wrote makes lots of sense. I had not heard about Rsleep, so that
> looks like interesting reading, thanks.
>
> I have often used Rfree as a simple tool to compare two protocols. If I am
> not actually optimising against Rfree but just using it for a one-off
> comparison then that is okay, right?
>
> Let's say I have two data processing protocols, A and B. Between these I
> might be exploring some difference in options within one data processing
> program, perhaps different geometry refinement parameters, or scaling
> options. I expect the A and B data sets to be quite similar, but I would
> like to evaluate which protocol was "better", and I want to do this
> quickly, ideally looking at a single number. I don't like I/sigI because I
> don't trust the sigmas, CC1/2 is often noisy, and I'm totally sworn off
> merging R statistics for these purposes. I tend to use Rfree as an
> easily-available metric, independent from the data processing program and
> the merging stats. It also allows a comparison of A and B in terms of the
> "product" of crystallography, namely the refined structure. In this I am
> lucky because I'm not trying to solve a structure. I may be looking at
> lysozyme or proteinase K: something where I can download a pretty good
> approximation to the truth from the PDB.
>
> So, what I do is process the data by A and process by B, ensure the data
> sets have the same free set, then refine to convergence (or at least, a lot
> of cycles) starting from a PDB structure. I then evaluate A vs B in terms
> of Rfree, though without an error bar on Rfree I don't read too much into
> small differences.
>
> Does this procedure seem sound? Perhaps it could be improved by randomly
> jiggling the atoms in the starting structure, in case the PDB deposition
> had already followed an A- or B-like protocol. Perhaps the whole approach
> is suspect. Certainly I wouldn't want to generalise by saying that A or B
> is better in all cases, but I do want to find a way to assess the various
> tweaks I can try in data processing for a single case.
>
> Any thoughts? I appreciate the wisdom of the BB here.
>
> Cheers
>
> -- David
>
>
> On Fri, 29 Oct 2021 at 15:50, James Holton  wrote:
>
>>
>> Well, of all the possible metrics you could use to asses data quality
>> Rfree is probably the worst one.  This is because it is a cross-validation
>> metric, and cross-validations don't work if you use them as an optimization
>> target. You can try, and might even make a little headway, but then your
>> free set is burnt. If you have a third set of observations, as suggested
>> for Rsleep (doi:10.1107/S0907444907033458), then you have a chance at
>> another round of cross-validation. Crystallographers don't usually do this,
>> but it has become standard practice in machine learning (training=Rwork,
>> validation=Rfree and testing=Rsleep).
>>
>> So, unless you have an Rsleep set, any time you contemplate doing a bunch
>> of random things and picking the best Rfree ... don't.  Just don't.  There
>> madness lies.
>>
>> What happens after doing this is you will be initially happy about your
>> lower Rfree, but everything you do after that will make it go up more than
>> it would have had you not performed your Rfree optimization. This is
>> because the changes in the data that made Rfree randomly better was
>> actually noise, and as the structure becomes more correct it will move away
>> from that noise. It's always better to optimize on something else, and then
>> check your Rfree as infrequently as possible. Remember it is the control
>> for your experiment. Never mix your positive control with your sample.
>>
>> As for the best metric to assess data quality?  Well, what are you doing
>> with the data? There are always compromises in data processing and
>> reduction that favor one application over another.  If this is a "I just
>> want the structure" project, then score on the 

[ccp4bb] coot problems on Mac with external display

[Ursula Schulze-Gahmen]

I apologize if this question has been raised before. But I am still
struggling with running Coot 0.95 on my mac laptop (Catalina) with an
external display.
Coot is functioning normal without the external display. But with external
display, the window for displaying models doesn't open properly. Is there a
fix for this situation?
I am using the Coot version from sbgrid, ccp4 7.1. I am running XQuartz
2.8.1 for the graphics.

Thanks

Ursula

-- 
Ursula Schulze-Gahmen, PhD
Staff Research Scientist
The J David Gladstone Institutes
1650 Owens St.
San Francisco, CA 94158
(415) 734 4835



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[ccp4bb] postdoctoral position available

[Srivastava, Dhiraj]

I am posting this advertisement on behalf of Prof. Nikolai Artemyev.


A postdoctoral position is available immediately at the Department of Molecular 
Physiology and Biophysics, University of Iowa Carver College of Medicine to 
study the molecular mechanisms of vertebrate visual transduction. We are using 
multiple approaches, including protein structure-function analysis, 
biochemistry, structural and molecular biology. A successful applicant will 
have a PhD, experience in biochemistry/structural and molecular biology, and a 
relevant publication record. Experience in x-ray crystallography and/or cryo-EM 
is preferred. Salary is commensurate with experience.

The University of Iowa is located in Iowa City, a dynamic college-town within 
driving distance of Chicago, St. Louis, and Minneapolis. Iowa City offers a 
culturally rich and highly academic environment supportive of the arts and 
sciences. The University of Iowa is part of the Molecular Biology Consortium 
that gives us substantial beam time for crystallographic studies at the 4.2.2 
ALS beamline (Lawrence Berkeley National Labs). We have active proposals at the 
Pacific Northwest Cryo-EM Center (PNCC) in Portland, OR.


Interested applicants should send a summary of previous research and a CV with 
names of at least two referees by e-mail to 
nikolai-artem...@uiowa.edu



Thank you
Dhiraj



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[ccp4bb] XFEL Crystallography Specialist Opportunity at Berkeley Lab

[Nicholas Sauter]

Lawrence Berkeley National Lab’s (LBNL ) Molecular
Biophysics & Integrated Bioimaging Division has an opening for an XFEL
Crystallography Specialist to join the team, either at the *Postdoctoral *or
*Project Scientist* level.



In this exciting role you will focus on X-ray free-electron laser (XFEL)
crystallography and software development.  The next decade of structural
biology at the Linac Coherent Light Source (LCLS) will include
groundbreaking advances in time domain work, diffuse scattering to observe
dynamic motion, and single particle diffraction. Considering the petabyte
scale of these data, we are undertaking ambitious collaborations with
structural biologists, light source facilities, and supercomputer centers
like Berkeley's National Energy Research Scientific Computing Center
(NERSC).



Projects will include 1) Photosystem II, discovering the sequence of redox
events leading to the release of molecular oxygen, using a combination of
time-resolved crystallography and X-ray emission spectroscopy; 2) Examining
the electronic environment of metalloenzyme catalytic metals; 3) New
methods for small-molecule structure determination.



What You Will Do:

   - Participate as the crystallography specialist on multidisciplinary
   teams.
   - Contribute to software development using our packages cctbx.xfel and
   dials as a starting point.
   - Develop a deep understanding of Exascale computing & GPU accelerators.
   - Interface with supercomputer design teams, computer science groups,
   LCLS beamline scientists, and X-ray crystallography user groups.
   - Derive algorithms to adapt to heterogeneous experimental designs.
   - Deliver new features on time and in support of structural biology.


   - Support scheduled beam time data collection at remote global
   facilities, in-person or online.


What is Required:

   - A working knowledge of crystallographic data collection, processing,
   molecular modeling, and model validation.
   - A publication record reflective of this experience.
   - Expertise with modern object-oriented, version-controlled software
   development, with a team-oriented approach.
   - Proficiency with Linux, Python, and C++.


Desired Qualifications:

   - Experience with GPU computing.
   - Experience in a high-performance computing environment.
   - Machine learning, for example TensorFlow or PyTorch experience.



*Positions are available at both the Postdoctoral and Project Scientist
levels:*

https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=94193
https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=94192



Based on University of California Policy - SARS-CoV-2 (COVID-19)
Vaccination Program and U.S Federal Government requirements, Berkeley Lab
requires that all members of our community obtain the COVID-19 vaccine as
soon as they are eligible. As a condition of employment at Berkeley Lab,
all Covered Individuals must Participate in the COVID-19 Vaccination
Program by providing proof of Full Vaccination or submitting a request for
Exception or Deferral. Visit covid.lbl.gov for more information.



Berkeley Lab is committed to Inclusion, Diversity, Equity and
Accountability (IDEA)  and
strives to continue building community with these shared values and
commitments. Berkeley Lab is an Equal Opportunity and Affirmative Action
Employer. We heartily welcome applications from women, minorities,
veterans, and all who would contribute to the Lab's mission of leading
scientific discovery, inclusion, and professionalism. In support of our
diverse global community, all qualified applicants will be considered for
employment without regard to race, color, religion, sex, sexual
orientation, gender identity, national origin, disability, age, or
protected veteran status.



Equal Opportunity and IDEA Information Links:

Know your rights, click here 
for the supplement: Equal Employment Opportunity is the Law and the Pay
Transparency Nondiscrimination Provision

under 41 CFR 60-1.4.


Nicholas K. Sauter, Ph. D.
https://biosciences.lbl.gov/profiles/nicholas-sauter/
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720



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Re: [ccp4bb] Senior scientist crystallographer position at Evotec

[Stephanie Duclos]

Dear CCP4 community,

We have several positions open in our two structural biology teams (Abingdon 
and Princeton).
If you are interested, please use the following links:


CryoEM Computational 
Scientist
 - Abingdon, UK



Crystallography Senior 
Scientist
 - Abingdon, UK



RNA Crystallography Senior 
Scientist
 - Abingdon, UK



Membrane Protein 
Crystallographer
 - Abingdon, UK



Senior Scientist- Structural 
Biology
 - Princeton, New Jersey, USA


Best wishes,

Stephanie


[cid:image002.png@01D41934.D23B4340]
Stephanie Duclos, Ph.D.
Team Leader, Structural Biology
+44 (0)1235 44 1548  (Direct)
stephanie.duc...@evotec.com
www.evotec.com

Evotec (UK) Ltd.
114 Innovation Drive,
Milton Park
Abingdon
Oxfordshire
OX14 4RZ, UK



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[ccp4bb] PDRA positions at Diamond and Essex

[Owen, Robin (DLSLtd,RAL,LSCI)]

Dear all,

We have two PDRA positions to work in the rapidly developing area of use of 
photocages for time-resolved serial crystallography at both Diamond and X-Ray 
Free Electron Lasers. One position is based at Diamond with Mike Hough and 
Robin Owen with the second based at the University of Essex in the lab of 
Jonathan Worrall.

This is an excellent opportunity to work on development of new approaches that 
will define how we can best collect both serial synchrotron crystallography 
data at I24 and Diamond in years to come as well as serial femtosecond 
crystallography data at XFEL sources. The post at Diamond will focus on 
beamline hardware and methods development. The successful candidate will work 
closely with the person in post at Essex who will be responsible for 
development of pipelines for production and crystallisation of several copper 
and iron containing proteins, with both PDRAs contributing to determination of 
time resolved movies of enzyme catalysis.

To apply and for further information see the links below. If you have any 
questions or would like to discuss further please feel free to drop me an email.

Essex: Senior research 
officer
 (closing date 10/11/21)
Diamond: PDRA Serial 
Crystallography
  (closing date 14/11/21)

All the best,
Robin



Dr Robin Owen
Principal Beamline Scientist
I24, Microfocus Macromolecular Crystallography
Diamond Light Source, UK
Tel: +44 1235 778522
http://www.diamond.ac.uk/Beamlines/Mx/I24.html


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