Add biomtSet option the sym command

[jacob_r_anderson@…]

Begin forwarded message:

From: "Anderson, Jacob via ChimeraX-users" <chimerax-users@…>
Subject: [chimerax-users] Feature Request From Chimera
Date: April 4, 2022 at 10:49:55 AM PDT
To: "chimerax-users@…" <chimerax-users@…>

Love ChimeraX - the UI is really enjoyable!

I was curious if I could put in a plug for biomtSet true option to be ported to ChimeraX's sym command! I expect a lower priority, but would love to use this tool in ChimeraX in some future version.

[Tom Goddard]

Eric, are the REMARK records from AtomicStructure.metadata written out to PDB files?

[Tom Goddard]

ChimeraX primarily uses mmCIF format since the PDB has long deprecated use of the old PDB format. So it is more likely we would add ability to put symmetry matrices into written out mmCIF files.

[Eric Pettersen]

Yes, they are.

Replying to Tom Goddard:

Eric, are the REMARK records from AtomicStructure.metadata written out to PDB files?

[Greg Couch]

Also asked on ResearchGate by James Hodgkinson-Bean: ​https://www.researchgate.net/post/Embedding_biological_assemblies_into_mmCIF_model_files

[Tom Goddard]

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 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.

Here's an example,

open 1a0m
sym #1 C5 add 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.