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<div class="moz-cite-prefix">Dear William,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you very much for your e-mail!
Your reports are very valuable, because they show us what the
requirements and priorities of COD users are.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">The problems that you have identified
are indeed problems with the COD data, mostly stemming from the
original publications. These issues, as well as some other ones,
can detected by using CIF validation software [1]. The problem is
that there is a large amount (> 11 mnl.) of these validation
issues [2], so we can not fix them on the spot; we are slowly
going through the COD one file at a time and fixing them, quite
often manually. In many cases we need to consult original
publications to see what the authors' intent really was, since the
main principle of the COD is "do not invent data".</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">It would be great of you could send us
your processing logs with all entries; we would use it as a guide
on what types of errors to treat first, and also I would be
interested to see if you catch more errors than we do. So yes,
please send us the remaining entry list of that is possible. Of
course I can not promise that we fix them immediately, but at
least we put them on the top of our priority queue ;). Also, some
problems might be impossible to fix; e.g. the COD entry 2005961
indeed has a broken _atom_site_aniso list, but the same problem is
detected also in the original supplementary data, and the paper
itself does not contain Uij list (as far as I could see). In this
case we can only mark the entry as "having problems", and suggest
the users to use only the XYZ coordinates and Uiso values instead;
or try to contact the authors and ask them for a correction or for
Fobs data so that the Uij values can be refined anew.<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Sincerely yours,<br>
Saulius<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Refs.:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">
<div class="moz-cite-prefix">[1] Vaitkus A. Validation messages
for the COD entry 1506432. URL:
<a class="moz-txt-link-freetext" href="https://sql.crystallography.net/db/cod_validation/validation_issue?offset=0&rows=100&filter=%28cod_id%20%3D%20%221506432%22%29">https://sql.crystallography.net/db/cod_validation/validation_issue?offset=0&rows=100&filter=%28cod_id%20%3D%20%221506432%22%29</a><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
[2] Vaitkus, A. COD validation issue database. 2021, URL: <a
href="http://sql.crystallography.net/db/cod_validation"
target="_blank" class="moz-txt-link-freetext">https://sql.crystallography.net/db/cod_validation</a>
[accessed 2022-11-15T17:39+02:00]. NOTE: the page is slow to load,
please be patient!</div>
<div class="moz-cite-prefix"><br>
</div>
On 2022-11-07 20:47, William Lenthe wrote:<br>
<blockquote type="cite"
cite="mid:SN1PR07MB3902048EFD350C1E229FE75A883C9@SN1PR07MB3902.namprd07.prod.outlook.com">
<p class="MsoNormal">I read through the first 100k entries of the
COD to test some cif parsing code and believe I found a few
errors<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">1506432: line 186 >F40 should be F40<o:p></o:p></p>
<p class="MsoNormal">1506503: line 200 >F1' should be F1'<o:p></o:p></p>
<p class="MsoNormal">2005854: lines 160-162 are human readable but
non-standard (should be split into 2 lines each or maybe the
more common As1/P1)<o:p></o:p></p>
<p class="MsoNormal">2005923: line 176 _atom_site_aniso_label is
'5' (maybe it should be O5?)<o:p></o:p></p>
<p class="MsoNormal">2005926: line 179 label is 04 instead of O4
(number zero instead of letter O)<o:p></o:p></p>
<p class="MsoNormal">2005961: _atom_site_aniso_label loop appears
to be malformed<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I generated another ~75 warnings if useful,
they are mostly issues with case consistency or atoms listed in
_atom_site_aniso_label that don’t appear in _atom_site_label<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
Dr. Saulius Gražulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366
</pre>
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