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<p>Hi, Bob!</p>
<p>How are you?</p>
<p>I'm currently doing COD data validation, and I'm running into two
issues that I would need your help to resolve.</p>
<p>1. Some AMCSD entries (e.g. COD ID 9015515 [1], AMCSD ID
"0019710" [2]) have recently received the '_atom_site_aniso_[]'
loop. This is great, but in some cases atom site labels in the
_atom_site_[] loop do not match:</p>
<p>
<blockquote type="cite">
<pre>loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
# ...
<b><font color="#ef2929">Pb'</font></b> 0.03159 0.03245 0.01811 0.01856 -0.00932 -0.00819
# ...
</pre>
</blockquote>
</p>
<p>vs.:</p>
<p>
<blockquote type="cite">
<pre>loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_U_iso_or_equiv
# ...
<font color="#ef2929"><b>Pb*</b></font> 0.10313 0.33075 0.34924 0.19800 0.02774
# ...</pre>
</blockquote>
</p>
<p>Can I assume that the atoms with quotes and atoms with stars are
the same, e.g. that "Pb'" and "Pb*" is the same atom?</p>
<p>I have written a script to fix this under the above-mentioned
assumptions, and I'm about to commit the changes to the COD. It
would be great to propagate these changes back to AMCSD, what you
think?</p>
<p>(Actually, I had the same issue with atom names containing
hyphens, e.g. 'OH1' and 'O-H1', but I see that this issue is
already fixed in AMCSD; I've updated the COD accordingly :).<br>
</p>
<p>2. In some places (56 COD entries) there are duplicate atom
labels. When these are in two loops, we can not decide
unambiguously which ANISO entry pertains to which atom. Example
(from COD ID 9000543 [3], AMCSD ID "0000554"):</p>
<p>
<blockquote type="cite"><font face="monospace">loop_<br>
_atom_site_aniso_label<br>
_atom_site_aniso_U_11<br>
_atom_site_aniso_U_22<br>
_atom_site_aniso_U_33<br>
_atom_site_aniso_U_12<br>
_atom_site_aniso_U_13<br>
_atom_site_aniso_U_23<br>
# ...<br>
<font color="#ef2929"><b>Mg</b></font> 0.00977 0.01092 0.00940
0.00000 0.00000 0.00000<br>
<font color="#ef2929"><b>Mg</b></font> 0.01490 0.00863 0.00956
0.00008 -0.00278 0.00053<br>
# ...</font><br>
</blockquote>
</p>
<p>and</p>
<p>
<blockquote type="cite">
<pre>loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
# ...
<font color="#ef2929"><b>Mg</b></font> 0.00720 0.39590 0.50000 0.21400
<font color="#ef2929"><b>Mg</b></font> 0.25000 0.50000 0.25000 1.00000
# ...</pre>
</blockquote>
</p>
<p>Can I assume, in general, that the atoms in both loops in the
same order, and number them 'Mg1' and 'Mg2' correspondingly? Like
this:</p>
<p> </p>
<blockquote type="cite"><font face="monospace">loop_<br>
_atom_site_aniso_label<br>
_atom_site_aniso_U_11<br>
_atom_site_aniso_U_22<br>
_atom_site_aniso_U_33<br>
_atom_site_aniso_U_12<br>
_atom_site_aniso_U_13<br>
_atom_site_aniso_U_23<br>
# ...<br>
<font color="#4e9a06"><b>Mg</b><b>1</b></font> 0.00977 0.01092
0.00940 0.00000 0.00000 0.00000<br>
<font color="#4e9a06"><b>Mg</b><b>2</b></font> 0.01490 0.00863
0.00956 0.00008 -0.00278 0.00053<br>
# ...</font><br>
</blockquote>
<p></p>
<p>and</p>
<p> </p>
<blockquote type="cite">
<pre>loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
# ...
<font color="#4e9a06"><b>Mg</b><b>1</b></font> 0.00720 0.39590 0.50000 0.21400
<font color="#4e9a06"><b>Mg</b><b>2</b></font> 0.25000 0.50000 0.25000 1.00000
# ...</pre>
</blockquote>
<p></p>
<p></p>
<p>I would do this for the COD (probably manually). Again, it would
be great to back-propagate these changes to the AMCSD collection.
I can send you the lists of changed files or the list of
problematic entries of the would help.<br>
</p>
<p>Cheers,<br>
Saulius<br>
</p>
<p>Refs.:</p>
<p>[1] <a class="moz-txt-link-freetext" href="http://www.crystallography.net/cod/9015515.cif">http://www.crystallography.net/cod/9015515.cif</a>,
<a class="moz-txt-link-freetext" href="http://www.crystallography.net/cod/9015515.html">http://www.crystallography.net/cod/9015515.html</a></p>
<p>[2]
<a class="moz-txt-link-freetext" href="https://rruff.geo.arizona.edu/AMS/CIF_text_files/05517_cif.txt">https://rruff.geo.arizona.edu/AMS/CIF_text_files/05517_cif.txt</a><br>
</p>
<p>[3] <a class="moz-txt-link-freetext" href="http://www.crystallography.net/cod/9000543.cif">http://www.crystallography.net/cod/9000543.cif</a>,
<a class="moz-txt-link-freetext" href="http://www.crystallography.net/cod/9000543.html">http://www.crystallography.net/cod/9000543.html</a><br>
</p>
<p>[4]
<a class="moz-txt-link-freetext" href="https://rruff.geo.arizona.edu/AMS/CIF_text_files/00635_cif.txt">https://rruff.geo.arizona.edu/AMS/CIF_text_files/00635_cif.txt</a><br>
</p>
<pre class="moz-signature" cols="72">--
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366
</pre>
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