[chimerax-users] save symmetry information to cif header

[Tom Goddard]

Yes it is the current ChimeraX daily builds on the download page.

	Tom


> On Sep 15, 2022, at 12:16 PM, Pranav Shah <p.shah.lab at gmail.com> wrote:
> 
> Thanks, I will take a look. Is this in the nightly build now?
> Best,
> Pranav
> --
> Pranav Shah
> Postdoctoral Research Fellow.
> 
> Division of Structural Biology,
> Wellcome Trust Centre for Human Genetics,
> University of Oxford,
> Roosevelt Drive, Oxford OX3 7BN,
> UK
> 
> On Thu, Sep 15, 2022 at 2:47 AM Tom Goddard <goddard at sonic.net> wrote:
>> 
>> Hi Pranav,
>> 
>>  I added an option to the ChimeraX sym command addMmcifAssembly that adds the assembly made by the sym command to the structure's metadata so if it is later written out to an mmCIF file it will have the assembly in the mmCIF tables. The name of the assembly will be "author defined assembly" and it will be appended to the list of already defined assemblies. There is no option to delete the previously defined assemblies (although you could edit the mmCIF file to remove them). The assembly information is added to the model that the sym command was run on, and also if it produces a new model but using graphical instances that model also gets the assembly information. If the sym command makes a whole set of new models at each of the symmetry positions, those copies don't get the assembly information (since the copies can be saved in a multimodel mmCIF file).
>> 
>> Here's an example,
>> 
>> open 1a0m
>> sym #1 C5 addMmcifAssembly true
>> save test.cif model #1
>> 
>> I have not added an option to output BIOMT matrices into the legacy PDB format (*.pdb). We focus on use of mmCIF in ChimeraX.
>> 
>> 
>> Tom
>> 
>> 
>> On Sep 12, 2022, at 11:26 AM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> I will try this week to add an option to write out the assembly information created with the sym command into mmCIF files.
>> 
>> Tom
>> 
>> 
>> On Sep 9, 2022, at 5:46 AM, Pranav Shah <p.shah.lab at gmail.com> wrote:
>> 
>> Hi Greg, Hi Tom,
>> I should have been a little bit more clear about the request. The
>> primary motivation for requesting this feature was that I had measured
>> the symmetry of the map which I later applied to the model (the
>> asymmetric unit had already been fit into the map).
>> Writing out the position matrices to a file would be a desired outcome
>> as saving the entire symmetric assembly is not always necessary.
>> Best,
>> Pranav
>> --
>> Pranav Shah
>> Postdoctoral Research Fellow.
>> 
>> Division of Structural Biology,
>> Wellcome Trust Centre for Human Genetics,
>> University of Oxford,
>> Roosevelt Drive, Oxford OX3 7BN,
>> UK
>> On Fri, Sep 9, 2022 at 12:53 AM Greg Couch <gregc at cgl.ucsf.edu> wrote:
>> 
>> 
>> Just to clarify, for mmCIF files, currently ChimeraX can write out the assembly position matrices, but only if they were present when reading in the mmCIF file.  Tom is proposing that the sym command optionally add the new assembly position matrices to the molecule's metadata so they will be written out.
>> 
>>  -- Greg
>> 
>> On 9/8/22 14:28, Tom Goddard via ChimeraX-users wrote:
>> 
>> Hi Pranav,
>> 
>> ChimeraX currently does not write out the assembly position matrices when saving mmCIF (.cif) or PDB (.pdb) format files.  But it probably could be added.  We have that as a feature request
>> 
>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6538
>> 
>> Here is how I'd envision that working.  You use the ChimeraX sym command to make symmetric copies of the asymmetric unit, then you save in mmCIF format.  It would write the mmCIF tables pdbx_struct_assembly, pdbx_struct_assembly_gen, pdbx_struct_oper_list to encode the positions of the symmetric copies.  I don't know of other software that reads these tables except for ChimeraX.  When you opened the written mmcif file in ChimeraX you would be able to to reproduce the symmetry with a command like "sym #1 assembly 1".
>> 
>> Is that what you had in mind?
>> 
>> Tom
>> 
>> 
>> On Sep 8, 2022, at 5:44 AM, Pranav Shah via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi Team,
>> 
>> Is it possible to insert BIOMT like fields into the asymmetric unit of
>> a symmetric molecule when saving the coordinates as a cif file?
>> Best,
>> Pranav
>> --
>> Pranav Shah
>> Postdoctoral Research Fellow.
>> 
>> Division of Structural Biology,
>> Wellcome Trust Centre for Human Genetics,
>> University of Oxford,
>> Roosevelt Drive, Oxford OX3 7BN,
>> UK
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>