As you know, the entity_poly_seq table says which polymeric residues are adjacent to each other (entity_poly_seq.num values are the atom_site.label_seq_id values). Without that information, ChimeraX still needs the atom_site.label_seq_id to imply the polymeric ordering. It also helps to give an atom_site.label_entity_id, even if the entity table is missing, to imply chain breaks. So in your case, give the first residue a label_seq_id of 1, and monotonically increase it for each following residue. If there is a gap, increase it by 2 or more. If ChimeraX doesn't figure out the gap correctly, it would be a bug. An alternative, that I have not tried, would be to give all of the inter-residue bonds explicitly in the struct_conn table. (Not sure if the residues would be merged into a single chain -- so it would be visually fine, but ChimeraX's internal data structures might be confused.) HTH, Greg On 7/6/2020 4:01 PM, Marcin Wojdyr wrote:
Hi, I'd like to generate mmCIF files (using my own software) that can be read by Chimera. The problem is that sometimes I don't know the full sequence (SEQRES), so I don't know values for _atom_site.label_seq_id.
If I skip label_seq_id entirely, the file doesn't load. ChimeraX gives warning: "Skipping atom_site category: Missing column 'label_seq_id'".
If I set all label_seq_id values to null ('.') I get warning: "Unable to infer polymer connectivity due to unspecified label_seq_id for residue "ARG" near line 125" and all residues are disconnected.
How should the mmCIF look like so that Chimera infers the connectivity in the same way as it does for PDB files?
Cheers, Marcin _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users