Re: [ccp4bb] keyword for refmac to output coordinates in cif format

[Ian Tickle]

Hi Mark

This tells you how to do it:

https://www.wwpdb.org/deposition/PDBxDeposit

Cheers

-- Ian



On Sat, 30 Oct 2021, 00:04 Mark J. van Raaij, 
wrote:

> Dear All,
>
> this may be something simple but I can’t find it in the CCP4i GUI or
> online.
> Is there a keyword to make refmac output the coordinates as a cif file
> instead of a pdb file - or better, as both?
> Or is it some other program that converts the formats?
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
>
> 
>
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Re: [ccp4bb] keyword for refmac to output coordinates in cif format

[Mark J. van Raaij]

sorry, you can ignore my question.
The mmcif file is output all along, for some reason I had never noticed it.
how stupid of me...

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
Section Editor Acta Crystallographica F
https://journals.iucr.org/f/


> On 30 Oct 2021, at 01:03, Mark J. van Raaij  wrote:
> 
> Dear All,
> 
> this may be something simple but I can’t find it in the CCP4i GUI or online.
> Is there a keyword to make refmac output the coordinates as a cif file 
> instead of a pdb file - or better, as both?
> Or is it some other program that converts the formats?
> 
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> 
> 
> 
> 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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[ccp4bb] keyword for refmac to output coordinates in cif format

[Mark J. van Raaij]

Dear All,

this may be something simple but I can’t find it in the CCP4i GUI or online.
Is there a keyword to make refmac output the coordinates as a cif file instead 
of a pdb file - or better, as both?
Or is it some other program that converts the formats?

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain



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[ccp4bb] Scientists positions open in Structural Genomics

[Karla J. F. Satchell]

The Northwestern Feinberg School of Medicine is seeking Two Protein Expression, 
Purification, and Crystallization Experts with an open rank for PostDoc, 
Research Associate, or Senior Research Associate to participate in a Structural 
Genomics Research Center addressing important biochemical studies related to 
infectious diseases. Protein targets are predominantly bacterial with some 
viral studies (included SARS-CoV-2) in topics of pathogenesis, antimicrobial 
resistance, and drug discovery.
https://www.feinberg.northwestern.edu/sites/csgid

Apply online at
LinkedIn : https://www.linkedin.com/jobs/view/2635721822 


>  Or Indeed:  
> https://www.indeed.com/viewjob?t=protein+purification+and+crystallization+expert=1162eea8c90cba54&_ga=2.265624143.1132066821.1635528688-1822760391.1635528688
>  
> 

Duties will include design of plasmids for commercial synthesis, protein 
expression and purification, and protein crystallization. Crystallography 
experience is helpful although this person will work closely with experienced 
crystallographers and thus this crystallographic data collection and analysis 
is not essential.
Communication skills are important as person will work directly with persons 
from outside labs to pursue studies. Ability to work with other team members to 
create a positive working environment is essential.

Two positions will remain open until filled. One position will emphasize design 
and conduct of High Throughput/Multiplex protein purification and 
crystallization so HTP experience is helpful. One position will emphasize high 
priority community targets with possibility to conduct biophysics/drug 
discovery research studies to support findings in structures.

Additional positions may open in spring/summer 2022 so candidates who do not 
expect to be available until mid 2022 encouraged to inquire now for future 
consideration.

It is expected that candidates will either hold a Ph.D. or have a minimum of 
six years relevant experience in protein purification and crystallization, 
preferably in a large center or company setting. More experienced candidates 
encouraged to apply. 

Northwestern University is an Equal Opportunity, Affirmative Action Employer of 
all protected classes, including veterans and individuals with disabilities. 
Women, racial and ethnic minorities, individuals with disabilities, and 
veterans are encouraged to apply. Hiring is contingent upon eligibility to work 
in the United States.

Job Type: Full-time
Pay: starts at $52,000 per year. Salary will be set competitive with experience 
level.
COVID-19 considerations:
Please see current Northwestern policy on COVID-19 at 
https://www.northwestern.edu/coronavirus-covid-19-updates/health/vaccine/

Karla J. F. Satchell, Ph.D.
Anne Stewart Youmans Professor of Microbiology,
Northwestern University Feinberg School of Medicine
PI & Co-Director, Center for Structural Genomics of Infectious Diseases
Dept. of Microbiology-Immunology
303 E. Chicago Avenue, Ward 6-205
Chicago, IL 60611
312-503-2162
k-satch...@northwestern.edu








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smime.p7s
Description: S/MIME cryptographic signature

[ccp4bb] postdoc position cryo-EM available (Bajic lab, New York)

[Goran Bajic]

We are looking for a postdoctoral candidate with experience in single-particle 
cryo-EM and willingness to learn virology and immunology. 
Ph.D. in Biochemistry, Biophysics or a related discipline is required. 
Tomography (cryo-ET) experience is an asset but not a pre-requisite.
The Bajic lab uses structural biology (cryo-EM and X-ray crystallography), 
virology and immunology approaches to answer fundamental, mechanistic questions 
in immune responses to viral pathogens. The
position is for a postdoctoral trainee interested in host immune recognition 
mechanisms of influenza, SARS-CoV-2, Chikungunya, and other viruses.

The position is available as soon as possible, but the start date is negotiable.

Lab Website: https://www.bajiclab.org/ 
Twitter: @gogo_science

Find out more about our department: 
https://icahn.mssm.edu/about/departments/microbiology 


To apply, send your C.V., cover letter, and contact information for 3 
references directly to Dr. Bajic.


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[ccp4bb] LINXS Workshop-Structural Resolution of Membrane Proteins: From Sample Preparation to Structural Resolution"

[Swati Aggarwal]

Dear All,

We are organizing the second part of the workshop series on 'Sample
preparation of membrane proteins*'* along with the Lund Institute Of
Advanced Neutron And X-Ray Science (LINXS).


In our first online workshop in May 2021, we discussed several aspects of
expression systems, protein purification, membrane solubilization and other
preparation methods. Our winter workshop is the continuation to further
explore topics related to the *“Structural Resolution of Membrane Proteins:
>From Sample Preparation to Structural Resolution”.*

*This workshop will be a hybrid meeting where we would like to meet several
attendees in Lund but also give the opportunity to those who can´t travel
to join us online. *





*Where: Lund (limited number of attendees) and online When: December 7th –
8th (noon-to-noon) CET 2021 Abstract submission deadline: 25th November
2021 Registration deadline: 1st December 2021 Workshop fee: Physical
participation - 600 SEK / 400 SEK (PhD students) Digital participation - No
fee*Preliminary Programme

*Day 1: Sample Preparation, Quality Control*

   -

   Multi-protein complexes, lipid-protein / enzyme-ligand interactions,
   orphan receptors
   -

   Membrane solubilization and other preparation methods
   -

   Detergent trials and functional characterization
   -

   Crystallisation techniques such as LCP and Hi-LIDE
   -

   Confirmed speakers: *Maria Marta Garcia Alai *(EMBL, Hamburg), *Petra
   Fromme* (Arizona State University), *Gisela Branden* (University of
   Gothenburg),

*Day 2: Output/Structural Resolution*

   -

   Serial crystallography
   -

   Electron diffraction
   -

   X-ray/Neutron scattering, X-ray crystallography for large proteins
   -

   Data collection and processing, molecular dynamics and new softwares
   -

   SEC-SAXS to study MP-detergent interaction
   -

   Confirmed speakers: *Christian Löw *(EMBL Hamburg), *Lise Arleth
*(Copenhagen
   University), *Erik Lindahl* (Stockholm University)


*For more information:*
https://www.linxs.se/events/2021/12/7/linxs-event-2nd-membrane-protein-working-group-workshop


Kind Regards,
The LINXS Organising Team



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

[James Holton]

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 resolution where CC1/2 
hits your favorite value. For some that is 0.5, others 0.3. I tend to 
use 0.0 so I can cut it later without re-processing. Whatever you do 
just make it consistent.


If its for anomalous, score on CCanom or if that's too noisy the 
Imean/sigma in the lowest-angle resolution or highest-intensity bin. 
This is because for anomalous you want to minimize relative error. The 
end-all-be-all of anomalous signal strength is the phased anomalous 
difference Fourier. You need phases to do one, but if you have a 
structure just omit an anomalous scatterer of interest, refine to 
convergence, and then measure the peak height at the position of the 
omitted anomalous atom.  Instructions for doing anomalous refinement in 
refmac5 are here:

https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html

If you're looking for a ligand you probably want isomorphism, and in 
that case refining with a reference structure looking for low Rwork is 
not a bad strategy. This will tend to select for crystals containing a 
molecule that looks like the one you are refining.  But be careful! If 
it is an apo structure your ligand-bound crystals will have higher Rwork 
due to the very difference density you are looking for.


But if its the same data just being processed in different ways, first 
make a choice about what you are interested in, and then optimize on 
that.  just don't optimize on Rfree!


-James Holton
MAD Scientist


On 10/27/2021 8:44 AM, Murpholino Peligro wrote:
Let's say I ran autoproc with different combinations of options for a 
specific dataset, producing dozens of different (but not so different) 
mtz files...
Then I ran phenix.refine with the same options for the same structure 
but with all my mtz zoo

What would be the best metric to say "hey this combo works the best!"?
R-free?
Thanks

M. Peligro



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

[Clemens Vonrhein]

On Thu, Oct 28, 2021 at 06:28:05PM +0530, Shipra Bijpuria wrote:
> I would first look at the dataset stats and define a resolution range
> mainly based on I/sigI >1 and cc1/2 >0.5. Based on this, would take the
> good resolution datasets only.

Some probably obvious word of caution here: these (quite sensible)
suggestions will depend hugely on factors like (1) binning, (2)
definition of a particular data quality metric and sometimes (3) the
treatment of Friedel pairs in computing these values. When comparing
seemingly identical metrics (as labelled) from different
programs/pipelines you have to be careful and aware of the various
differences in implementation. If one is sure that these values are
computed in the same way with the same binning, comparisons will be
possible, yes.

Also, a lot (most?) datasets are poorly described with a single
resolution value, even it it is rather convenient for sorting ;-)

Just thought to add this for the record for future generations of
ccp4bb-archive searching crystallographers ;-)

Clemens



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