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 ?