[chimerax-users] CIF writer renumbers residues

[Greg Couch]

If your mmCIF input file is incomplete and the missing sequence 
information, then the mmCIF writer does not write it out either. The are 
too many ways to get it wrong and mislead the scientist. That said, I 
can envision adding a "best guess" option to the mmCIF writer someday.

As for the residue renumbering, there are two sets of residue numbers in 
a mmCIF file, the internal label_seq_id that is used to link the the 
atom_site table entries with other mmCIF tables.  And the auth_seq_id, 
which is the author assigned value.  The auth_seq_id written is the same 
as the one read in.

In your case, you should use the auth_seq_id for matching (assuming it's 
present, you could add it with the same value as the label_seq_id to 
your original mmCIF file).  Or, the original mmCIF file needs to supply 
the sequence information (the entity, entity_poly, and entity_poly_seq 
tables), so the gaps are known instead of guessed.  Or, perhaps ISOLDE 
could help you by inserting "unknown" gap residues in to the chain to 
preserve the numbering.

     HTH,

     Greg

On 6/23/2020 10:47 AM, Daniel Asarnow wrote:
> Hi all,
> When I save a CIF from ChimeraX (while using ISOLDE), the warning "Not 
> saving entity_poly_seq for non-authoritative sequences" is produced, 
> and all the residues have been sequentially renumbered from 1. When 
> there are missing residues, each segment has to be renumbered manually 
> afterwards. Is there some way to avoid this with PDB or CIF inputs? Is 
> it a bug?
>
> Best,
> -da
>