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<p>So it's not so simple. The auth_.... fields are not required,
they just happen to be in the files that the PDB provides. Other
programs can not be expected to provide them. The RCSB has
software that can validate mmCIF files against various
dictionaries: the MMCIF Dictionary Suite,
<a class="moz-txt-link-freetext" href="https://sw-tools.rcsb.org/apps/MMCIF-DICT-SUITE/index.html">https://sw-tools.rcsb.org/apps/MMCIF-DICT-SUITE/index.html</a>.
Programs that generate mmCIF files should verify that the
generated files are complete. And the dictionary used for
validation should be documented in the audit_conform table.<br>
</p>
<p>If your data is in the mmCIF format, you are better off using
ChimeraX than Chimera. The reader is orders of magnitude faster.
And I am working on fixing any bugs that come up :-). I have
documented the parts of mmCIF files that are important for
ChimeraX. For example, the Cartesian coordinates are required for
atoms. See
<a class="moz-txt-link-freetext" href="https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif.html">https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif.html</a>
-- in particular, read "ChimeraX Fast mmCIF Guidelines" and
"Writing mmCIF FIles in ChimeraX".</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 12/7/2018 12:47 AM,
<a class="moz-txt-link-abbreviated" href="mailto:moocow@mindless.com">moocow@mindless.com</a> wrote:<br>
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<div>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.</div>
<div> </div>
<div>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.</div>
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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.</p>
<p> HTH,</p>
<p> Greg</p>
<div class="moz-cite-prefix">On 12/6/18 4:03 AM, <a
class="moz-txt-link-abbreviated"
href="mailto:moocow@mindless.com"
onclick="parent.window.location.href='mailto:moocow@mindless.com';
return false;" target="_blank"
moz-do-not-send="true">moocow@mindless.com</a>
wrote:</div>
<blockquote>
<div style="font-family: Verdana;font-size: 12.0px;">
<div><font style="background-color:
rgb(255,255,255);">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>
</div>
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