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<p>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.</p>
<p>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.<br>
</p>
<p> HTH,</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 12/6/18 4:03 AM, <a class="moz-txt-link-abbreviated" href="mailto:moocow@mindless.com">moocow@mindless.com</a>
wrote:<br>
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cite="mid:trinity-abdfcd23-9fd9-4de1-87cd-f62e03207b0c-1544097838462@3c-app-mailcom-lxa09">
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<div><font style="background-color:#ffffff">An mmcif / numbering
question...<br>
When specifying residues, chimera seems to use "auth_seq_id"
(the authors' numbering), as well as the authors' naming of
chains (auth_asym_id).<br>
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) ?<br>
Is the label_xxx information discarded when chimera reads an
mmcif file or is it hidden in an attribute somewhere ?</font><br>
<br>
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