[chimerax-users] save symmetry information to cif header

[Greg Couch]

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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>
>
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