On Nov 3, 2023, at 8:26 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I have a cryoEM map that was generated with C7 symmetry enforced, with its symmetry axis parallel to the z axis in ChimeraX. I fetched a prediction from AlphaFoldDB and docked it in the map. So far, so good.

I can generate the other protomers with a command like this:

sym #1 C7 axis z center cofr

(assuming #1 is the single protomer from AlphaFoldDB, and the cofr is correctly lying on the symmetry axis, which I get sufficiently close if I center the view on the map)

Now, because symmetry was enforced for the map, it makes no sense to model, refine and store the entire heptamer. I should be able to do everything with a single protomer, and store relevant info as "biological assembly" so the heptamer can be regenerated from the protomer. At least if I am understanding this correctly.

I tried the above command, or this variant: sym #1 C7 axis z center cofr addMmcifAssembly true

And subsequently saving in PDB or mmCIF format, but none of this produces what I want, which is a file containing the single protomer + assembly info. I either get a file with the single protomer or a file with the heptamer, in both cases without any biological assembly info.

I looked up the options of the save command for PDB and mmCIF format, but found nothing that seemed relevant to this problem.

Is there a way to do this? Or am I misunderstanding something?

Related question: it might make sense to use the whole heptamer for refinement, so all interfaces between protomers "see" each other (probably important when using ISOLDE). What is the best way to deal with this? Build and refine the whole heptamer and save only a single protomer + assembly info at the very end? Or have the symmetry enforced from the beginning, throughout the whole refinement process, and really ever refine a single protomer? (7 times less work, so probably the preferred option).

Thank you in advance,

Guillaume

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