Files should use symmetry information if available

[kristen.browne@…]

When comparing QS for eg. https://www.rcsb.org/structure/2BTV, the QS is using the symmetry information to construct the full virus, but when uploading the mmCIF from the entry, it does not.  Phil has requested that if symmetry information is available in the mmCIF (or other data file) that it should be used.  Essentially a QS should look the same as if the user uploaded the mmCIF directly.

Please keep Phil cc’d on ticket as he’s better versed in the requirements for this 😊

Kristen Browne, MSc, MscBMC
Contractor – MSC, Inc. | A Guidehouse Company
3D Modeling and Biovisualization Specialist
Bioinformatics and Computational Biosciences Branch (BCBB)<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
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[Tom Goddard]

What is a "QS"?

I know that NIH 3D has been biological assemblies from PDBe, and that would provide the virus icosahedral symmetry for PDB 2BTV. If an mmCIF is submitted as a user-provided file instead of a PDB id code then the assembly information in the mmCIF file could be used. I think the NIH 3D ChimeraX scripts do use the sym command to make assemblies (I've seen an NIH 3D bug report that was using that).

I don't know what the ChimeraX NIH 3D scripts our currently doing to handle symmetry and Eric did all the work on those, so I am reassigning to Eric. I can advise if there is some question about the sym command, which I wrote.

[Eric Pettersen]

Yes, what is QS?

Given a PDB ID, it fetches it via pdbe_bio. Given a regular PDB or mmCIF file, it uses it as is. I take it that this request is to apply symmetry to the latter if the info is in the file? You don't feel that might be surprising to the user (or should be some kind of option)?

[kristen.browne@…]

QS is quicksubmit (an NIH 3D term for autogenerating models from a database ID).

Phil can comment about the use case as he is the originator of the request.

K

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From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Monday, December 12, 2022 1:30 PM
Cc: goddard@cgl.ucsf.edu; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #8170: Files should use symmetry information if available

#8170: Files should use symmetry information if available
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          Reporter:  kristen.browne@...  |      Owner:  pett
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         Component:  Input/Output      |    Version:
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Comment (by pett):

 Yes, what is QS?

 Given a PDB ID, it fetches it vis pdbe_bio.  Given a regular PDB or mmCIF  file, it uses it as is.  I take it that this request is to apply symmetry  to the latter if the info is in the file?  You don't feel that might be  surprising to the user (or should be some kind of option)?

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[Eric Pettersen]

It certainly seems possible that the user might want to print the asymmetric unit. Make it an option flag?

[Eric Pettersen]

But if you felt that wanted to print the asymmetric unit would be really rare, I can make the script always apply the symmetry information.

[Eric Pettersen]

wanted→wanting

[kristen.browne@…]

I checked with Phil, and, for now, he'd like to use the symmetry information by default (if available).  In the future we might add a flag and present the user with more flexible options, but that's a ways off for us.

Thanks!

K

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, December 13, 2022 4:35 PM
Cc: goddard@cgl.ucsf.edu; Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu; Cruz, Phil (NIH/NIAID) [C] <phil.cruz@nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #8170: Files should use symmetry information if available

#8170: Files should use symmetry information if available
---------------------------------------+----------------------
          Reporter:  kristen.browne@...  |      Owner:  pett
              Type:  defect            |     Status:  feedback
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         Component:  Input/Output      |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
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Changes (by pett):

 * status:  assigned => feedback


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[goddard@…]

An mmCIF model from the PDB often contains multiple assemblies.  I guess the plan would be to use the first assembly.  In the case of 2btv the first assembly is the full virus capsid.  There are 6 assemblies for 2btv, hexamer, pentamer, asym unit, different coordinate systems.  I am not sure if the PDB has any set pattern for how they are ordered.  Also the assemblies usually have names "1", "2", ... but they need not be numeric, I have seen P1 or letters.  The sym command requires giving an assembly name, filling an available name or even seeing if any assemblies exist may take some Python code.

[Eric Pettersen]

Okay, I have added a commit to the still-outstanding pull request to expand the symmetry of a submitted file if available. Note that that you really need to get a new daily build to use this effectively, because the step that combines the symmetry-generated models into a single model for processing can be very slow for large structures in previous builds.