[chimerax-users] label_seq_id in mmcif files for Chimera

[Greg Couch]

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
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