To answer the general question, ChimeraX doesn't yet have a way to set the full sequence for a mmCIF entity. See https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files for how to fix the mmCIF output from various refinement packages. For example, the Phenix has "mmtbx.prepare_pdb_deposition program to create a mmCIF file with the sequence".
In this particular case, where the starting structure is an Alphafold prediction with atoms for every residue in the full sequence, you can get the correct sequence into the mmCIF output with the "bestGuess" option. See https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#mmcif. I'd also recommend, in your case, using the computedSheets option. In older ChimeraX's, you need to run dssp before using computedSheets to get the helix information. In recent ChimeraX's (daily build and 1.7 release candidate), computedSheets will also output the helix information if it wasn't present in the input.
Adding a sequence with bestGuess can be deceiving of because
missing leading or trailing residues, or gaps of indeterminate
length. But in this case, you should be fine.
-- Greg
From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] How to save a sequence in an mmCIF file?
Date: November 29, 2023 at 2:45:31 AM PST
Reply-To: Guillaume Gaullier <guillaume.gaullier@kemi.uu.se>
Hello,
Starting from an AlphaFold prediction, I refined a model against a map with ISOLDE. I trimmed the segments not supported by any density. The resulting mmCIF file that I saved now opens with this warning:
Unknown polymer entity '1' near line 187
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Displaying the sequence of this chain shows the correct numbering (with jumps in numbering according to missing segments in the structure), but the sequence of the missing structure segments is not displayed.
When I open the fasta file containing the full-length sequence, the sequence gets automatically associated to the structure, and the sequence viewer annotates the segments with missing structure correctly. I would like to save this full-length sequence in my mmCIF file so the full-length sequence with annotated missing structure segments shows up next time I open this file. But when I try to save at this point, I get the following notice:
Not saving entity_poly_seq for non-authoritative sequences
The documentation for "save" and "sequence" didn't help. How can I make this sequence "authoritative" and save it into my mmCIF file?
Thank you in advance,
Guillaume
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