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

Greg Couch gregc at cgl.ucsf.edu
Thu Dec 6 14:52:56 PST 2018

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.



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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