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<div class="moz-cite-prefix">Hi, Bob,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you for the swift answer! Below
are m y answers and comments.<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2024-08-03 21:04, Downs, Robert T -
(rdowns) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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 that out. Looks like a labeling problem. Pb* and
Pb’ are the same atom. The Pb atoms are on a split site. </span></p>
</blockquote>
Thanks for the clarification! I also understood it the same way!<br>
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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
think that my code to write <span class="SpellE">cifs</span>
tried to avoid using a quote mark ‘ because it gets
interpreted poorly on some applications, especially when
searching, so I changed the quote to an asterisk, *, but I
must have only done it for atomic positions and didn’t do it
for the displacement factors. Ugh.</span></p>
</blockquote>
<p>So the single quote character ("'") is regularly changed to an
asterisk ("*") when converting from AMC to CIF format, right? And
yes, it should be the ASCII quote (ASCII DEC 39 / HEX 27), not the
Unicode quote "<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"">‘"
(UTF-8 HEX sequence: e2 80 98).</span></p>
<p><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"">As
far as the CIF and COD parser goes, the single ASCII quote in
atom names ("'") is as good (or bad) as the asterisk. It is
standard CIF, and the software MUST read it; if some program
does not, IMHO the program should be fixed, not the data file.
Adapting dat presentation to the quirks of buggy programs is,
IMHO, a bad strategy – next time some program will <i>insist</i>
(erroneously) on having a quote and will reject the asterisk,
and we are stuck :). Actually, all modern programs, notably
Jmol, can process atom names with terminating quotes, even
though this needs to use a new syntax in the program scripts...
Also, changing "'" to "*" makes AMC and CIF atom naming
different, so finding correspondences becomes more difficult.<br>
</span></p>
<p><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"">If
identifier-like atom labels are required, maybe it is better to
spell out 'prime' and 'doubleprime' in both AMC and CIF files?<br>
</span></p>
<p><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"">In
any case, there is a second problem related to asterisk
conversion: in several AMCSD CIFs (e.g. COD 9002008 [1], AMCSD
"0002070" [2]) two atoms Pb' and Pb" are present, which both
become Pb* after conversion:<br>
</span></p>
<p><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"">
<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>
<b>Pb'</b> 0.02100 0.05400 0.03400 -0.01300 0.00700 -0.00100<br>
<b>Pb"</b> 0.01900 0.08100 0.06100 0.00600 0.01200 0.00500</font><br>
</blockquote>
and</span></p>
<p><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"">
<blockquote type="cite">
<pre>loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
<b>Pb*</b> 0.27050 -0.01360 0.07260 0.59000
<b>Pb*</b> 0.27870 0.00890 0.06860 0.41000
</pre>
</blockquote>
Thus, it is no longer possible for CIF programs to tell which is
which without resorting to some wild assumptions (i.e. that the
CIF atoms follow the AMC file ordering and no program has
rearranged the atoms in the meantime...)<br>
</span></p>
<p>What would be your policy on handling double quotes in atom
labels? Are you going to leave them as double quotes, or maybe
convert to double asterisks, e.g. to "Pb**"?<br>
</p>
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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""><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"">Anyways,
its my mistake. Thanks for catching it.</span></p>
</blockquote>
A great deal of credit goes to Antanas Vaitkus who wrote the
'cif_validate' software – it is now very handy to catch such
situations in a systematic way :)<br>
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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""><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"">You
can go to
<span class="SpellE">amcsd</span> web site and see the <span
class="SpellE">amc</span> file, and that would have helped
you see the problem. I make
<span class="SpellE">cifs</span> from the <span
class="SpellE">amc</span> format.<o:p></o:p></span></p>
</blockquote>
<p>Thanks, great tip! I somehow overlooked this; we can use AMC
files to double check the CIFS!<br>
</p>
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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"">Also,
the atoms are always in the same order in the two parts of the
cif, (<span class="SpellE">xyz</span> and <span
class="SpellE">adf</span>) so that might help you to solve
issues. Its because the cif is always made from the
<span class="SpellE">amc</span>.</span></p>
</blockquote>
Excellent! Good to know, I'll use this info to restore the aniso
<-> atom_site connections.<br>
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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""><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
am considering how to change this somehow in the future. We
are building a new website for the future,
<span class="SpellE">amcsd</span> will become part of a NASA
host of mineral databases. I expect to have an agreement with
the society journals to automatically download their deposited
<span class="SpellE">cifs</span>. </span></p>
</blockquote>
This sounds very promising, cool!
<blockquote type="cite"
cite="mid:BY5PR19MB3746AFA45596515444F71693D3BC2@BY5PR19MB3746.namprd19.prod.outlook.com">
<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"">Unfortunately,
these <span class="SpellE">cifs</span> are usually so poorly
made that I know this will be a bad solution. It’s the reason
why I have always made
<span class="SpellE">amc</span> format and then computed the <span
class="SpellE">
cifs</span>. But I am planning for the future when it will
not be me doing the databases.</span></p>
</blockquote>
<p>Regarding the CIFs, we have at the COD a pretty decent pipeline
for ingesting CIFs, even some broken ones. Could that be useful?
Maybe we could collaborate on the CIF processing and reviewing?</p>
<p>Regards,<br>
Saulius<br>
</p>
<p>Refs.:</p>
<p>[1] <a class="moz-txt-link-freetext" href="http://www.crystallography.net/cod/9002008.cif">http://www.crystallography.net/cod/9002008.cif</a></p>
<p>[2]
<a class="moz-txt-link-freetext" href="https://rruff.geo.arizona.edu/AMS/CIF_text_files/02094_cif.txt">https://rruff.geo.arizona.edu/AMS/CIF_text_files/02094_cif.txt</a>,
<a class="moz-txt-link-freetext" href="https://rruff.geo.arizona.edu/AMS/AMC_text_files/02094_amc.txt">https://rruff.geo.arizona.edu/AMS/AMC_text_files/02094_amc.txt</a>,
<a class="moz-txt-link-freetext" href="https://rruff.geo.arizona.edu/AMS/result.php">https://rruff.geo.arizona.edu/AMS/result.php</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)
mobile: (+370-684)-49802, (+370-614)-36366
</pre>
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