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<p class="MsoNormal"><span style="mso-bidi-font-size:11.0pt;mso-ascii-font-family:Aptos;mso-hansi-font-family:Aptos;mso-bidi-font-family:"Times New Roman"">Saulius,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-bidi-font-size:11.0pt;mso-ascii-font-family:Aptos;mso-hansi-font-family:Aptos;mso-bidi-font-family:"Times New Roman"">I will replace every single quote in atom names in the entire database. You wont see the changes until
I rebuild it however, and that wont be for a month or so.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-bidi-font-size:11.0pt;mso-ascii-font-family:Aptos;mso-hansi-font-family:Aptos;mso-bidi-font-family:"Times New Roman"">Thanks for pointing in out to me. If you see any issues with double quotes let me know.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-bidi-font-size:11.0pt;mso-ascii-font-family:Aptos;mso-hansi-font-family:Aptos;mso-bidi-font-family:"Times New Roman"">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-bidi-font-size:11.0pt;mso-ascii-font-family:Aptos;mso-hansi-font-family:Aptos;mso-bidi-font-family:"Times New Roman"">Bob<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman"">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;mso-fareast-font-family:"Times New Roman""> Saulius
Gražulis <grazulis@ibt.lt> <br>
<b>Sent:</b> Saturday, August 3, 2024 3:49 AM<br>
<b>To:</b> Bob Downs <rdowns@u.arizona.edu><br>
<b>Cc:</b> cod-bugs@lists.crystallography.net; kicis@lists.crystallography.net<br>
<b>Subject:</b> [EXT] AMCSD duplicate atoms and missing aniso links?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p align="center" style="text-align:center;background:white"><strong><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:red;background:white">External Email</span></strong><b><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black;background:white"><o:p></o:p></span></b></p>
<p class="MsoNormal" style="background:white"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman";color:black"><o:p> </o:p></span></p>
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<p>Hi, Bob!<o:p></o:p></p>
<p>How are you?<o:p></o:p></p>
<p>I'm currently doing COD data validation, and I'm running into two issues that I would need your help to resolve.<o:p></o:p></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:<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>loop_<o:p></o:p></pre>
<pre>_atom_site_aniso_label<o:p></o:p></pre>
<pre>_atom_site_aniso_U_11<o:p></o:p></pre>
<pre>_atom_site_aniso_U_22<o:p></o:p></pre>
<pre>_atom_site_aniso_U_33<o:p></o:p></pre>
<pre>_atom_site_aniso_U_12<o:p></o:p></pre>
<pre>_atom_site_aniso_U_13<o:p></o:p></pre>
<pre>_atom_site_aniso_U_23<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
<pre><b><span style="color:#EF2929">Pb'</span></b> 0.03159 0.03245 0.01811 0.01856 -0.00932 -0.00819<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
</blockquote>
<p>vs.:<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>loop_<o:p></o:p></pre>
<pre>_atom_site_label<o:p></o:p></pre>
<pre>_atom_site_fract_x<o:p></o:p></pre>
<pre>_atom_site_fract_y<o:p></o:p></pre>
<pre>_atom_site_fract_z<o:p></o:p></pre>
<pre>_atom_site_occupancy<o:p></o:p></pre>
<pre>_atom_site_U_iso_or_equiv<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
<pre><b><span style="color:#EF2929">Pb*</span></b><span style="mso-spacerun:yes"> </span>0.10313<span style="mso-spacerun:yes"> </span>0.33075<span style="mso-spacerun:yes"> </span>0.34924<span style="mso-spacerun:yes"> </span>0.19800<span style="mso-spacerun:yes"> </span>0.02774<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
</blockquote>
<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?<o:p></o:p></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?<o:p></o:p></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 :).<o:p></o:p></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"):<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-family:"Courier New";mso-fareast-font-family:"Times New Roman"">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>
<b><span style="color:#EF2929">Mg</span></b> 0.00977 0.01092 0.00940 0.00000 0.00000 0.00000<br>
<b><span style="color:#EF2929">Mg</span></b> 0.01490 0.00863 0.00956 0.00008 -0.00278 0.00053<br>
# ...</span><span style="mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</blockquote>
<p>and<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>loop_<o:p></o:p></pre>
<pre>_atom_site_label<o:p></o:p></pre>
<pre>_atom_site_fract_x<o:p></o:p></pre>
<pre>_atom_site_fract_y<o:p></o:p></pre>
<pre>_atom_site_fract_z<o:p></o:p></pre>
<pre>_atom_site_occupancy<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
<pre><b><span style="color:#EF2929">Mg</span></b><span style="mso-spacerun:yes"> </span>0.00720<span style="mso-spacerun:yes"> </span>0.39590<span style="mso-spacerun:yes"> </span>0.50000<span style="mso-spacerun:yes"> </span>0.21400<o:p></o:p></pre>
<pre><b><span style="color:#EF2929">Mg</span></b><span style="mso-spacerun:yes"> </span>0.25000<span style="mso-spacerun:yes"> </span>0.50000<span style="mso-spacerun:yes"> </span>0.25000<span style="mso-spacerun:yes"> </span>1.00000<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
</blockquote>
<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:<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-family:"Courier New";mso-fareast-font-family:"Times New Roman"">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>
<b><span style="color:#4E9A06">Mg1</span></b> 0.00977 0.01092 0.00940 0.00000 0.00000 0.00000<br>
<b><span style="color:#4E9A06">Mg2</span></b> 0.01490 0.00863 0.00956 0.00008 -0.00278 0.00053<br>
# ...</span><span style="mso-fareast-font-family:"Times New Roman""><o:p></o:p></span></p>
</blockquote>
<p>and<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>loop_<o:p></o:p></pre>
<pre>_atom_site_label<o:p></o:p></pre>
<pre>_atom_site_fract_x<o:p></o:p></pre>
<pre>_atom_site_fract_y<o:p></o:p></pre>
<pre>_atom_site_fract_z<o:p></o:p></pre>
<pre>_atom_site_occupancy<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
<pre><b><span style="color:#4E9A06">Mg1</span></b><span style="mso-spacerun:yes"> </span>0.00720<span style="mso-spacerun:yes"> </span>0.39590<span style="mso-spacerun:yes"> </span>0.50000<span style="mso-spacerun:yes"> </span>0.21400<o:p></o:p></pre>
<pre><b><span style="color:#4E9A06">Mg2</span></b><span style="mso-spacerun:yes"> </span>0.25000<span style="mso-spacerun:yes"> </span>0.50000<span style="mso-spacerun:yes"> </span>0.25000<span style="mso-spacerun:yes"> </span>1.00000<o:p></o:p></pre>
<pre># ...<o:p></o:p></pre>
</blockquote>
<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.<o:p></o:p></p>
<p>Cheers,<br>
Saulius<o:p></o:p></p>
<p>Refs.:<o:p></o:p></p>
<p>[1] <a href="http://www.crystallography.net/cod/9015515.cif">
http://www.crystallography.net/cod/9015515.cif</a>, <a href="http://www.crystallography.net/cod/9015515.html">
http://www.crystallography.net/cod/9015515.html</a><o:p></o:p></p>
<p>[2] <a 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><o:p></o:p></p>
<p>[3] <a href="http://www.crystallography.net/cod/9000543.cif">
http://www.crystallography.net/cod/9000543.cif</a>, <a href="http://www.crystallography.net/cod/9000543.html">
http://www.crystallography.net/cod/9000543.html</a><o:p></o:p></p>
<p>[4] <a 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><o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Dr. Saulius Gražulis<o:p></o:p></pre>
<pre>Vilnius University Institute of Biotechnology, Saulėtekio al. 7<o:p></o:p></pre>
<pre>LT-10257 Vilnius, Lietuva (Lithuania)<o:p></o:p></pre>
<pre>fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353<o:p></o:p></pre>
<pre>mobile: (+370-684)-49802, (+370-614)-36366<o:p></o:p></pre>
<p class="MsoNormal"><span style="mso-fareast-font-family:"Times New Roman""><br>
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