Thanks for the explanation. The water-numbering argument is convincing as a reason to use author_... fields. I think these also correspond with the fields in the old pdb format.

I can see the PDB's logic in using a flexible format with room to put in every conceivable piece of information, but one can wonder if they really did the world a favour. It is almost guaranteed that this program will use author_.. fields and that program will use label_... fields.

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@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 ?