[Chimera-users] mmcif, auth_xx information versus label_xx information

[Greg Couch]

Yes, Chimera uses the author's numbering because that it what is used in 
the author's publication.  It turns out that this is especially 
important for waters since the PDB/RCSB refuses to number waters in the 
label_seq_id field which breaks the one-to-one mapping of (label_seq_id, 
label_asym_id) to a residue.

In Chimera, the mapping with label_seq_id is discarded after is it 
used.  In ChimeraX, there is no UI for label_seq_id, but, in Python 
code, the nth residue in a Chain instance is label_seq_id n.  And 
residues have a mmcif_chain_id attribute which is the label_asym_id.  So 
it is possible to reconstruct the mapping if need be.

     HTH,

     Greg

On 12/6/18 4:03 AM, moocow at mindless.com wrote:
> An mmcif / numbering question...
> When specifying residues, chimera seems to use "auth_seq_id" (the 
> authors' numbering), as well as the authors' naming of chains 
> (auth_asym_id).
> Is there any way to ask chimera to find residues using "label_seq_id" 
> and "label_seq_id" (the numbering the protein data bank gives) ?
> Is the label_xxx information discarded when chimera reads an mmcif 
> file or is it hidden in an attribute somewhere ?
>
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