<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<div class="moz-cite-prefix">Dear Eduardo,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you very much for your e-mail,
for offering your work for COD, and my big apologies for not
responding earlier.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Your structure seems to be the all time
record at the COD :); all structures deposited so far seem to fit
the previous 2M limit. I have thus increased the upload limit to
20M, so that your structure can be uploaded both zipped and
unzipped (as a plain CIF file). Please check if this works for
you.<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">I have also looked into the CIF itself
(just to see if the upload problem was not related to the content
itself). May I suggest several changes to the CIF:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">1) The original file file contained
characters with diacritics ("ü" in
"_computing_molecular_graphics 'shelXle (Hübschle, Sheldrick and
Dittirch, 2011)'"), entered in the Latin1 encoding. Such
characters are not permitted in the CIF standard and are in fact
ambiguous. While our COD software will change them to a CIF
compliant sequence using an XML entity, I suggest that a better
encoding is used – the CIF escape sequence ('H\"ubschle' instead
of 'Hübschle'). If you accept this suggestion, I have prepared a
file under a private link with this change [1] link for your
convenience;</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">2) certain disorder groups generate
atoms that have steric clashes when interpreted as distinct
molecules. The disorder is notoriously tricky to mark up in CIF,
especially since you have disorder around a special position for
one water molecule. If you would agree with such interpretation of
your structure, I have prepared the file with the new disorder
markup [2]; I also attach detailed descriptions of the changes
("notes-SG.txt"), which you may want to ingest into your work
flow. This new markup gives chemically complete molecules when
they are generated from each disorder assembly (at least with our
software), so would be beneficial IMHO.<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">3) finally, I have noticed that one
atom, C15", lacks hydrogen atoms, but seems to need them, being a
methylene bridge (it is an alternative conformation of the C15F
that does have two hydrogens attached). May I suggest that you
model hydrogens on C15", so that every disorder group has the same
composition? This can be done in two ways:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">3a) Adding the hydrogens model
explicitly and re-running SHELX analysis to get the (slightly)
updated statistics (R-factors et al.);</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">3b) Adding the new data name to the
coordinate loop, '_atom_site_attached_hydrogens', specifying '.'
for all atoms except the C15" atom, and giving value '2' for the
'_atom_site_attached_hydrogens' of atom C15". This would formally
not require re-computation of R-factors. I have prepared an
example of such encoding in [3].<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">The change suggested in (3) would add
one hydrogen to your structure (2 half occupied H sites), and thus
change the formula from 'C254 <b><i>H404</i></b> N14 O72 U8' to
'C254 <b>H405</b> N14 O72 U8'. The latter formula, however, would
agree with individual formulae of each disordered assembly
collection:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">
<blockquote type="cite"><font face="monospace">saulius@tasmanijos-velnias
COD-deposition-big-file/ $ cif_molecule --one-datablock
C3ok-charset-OK-mark-disorder-attached-hydrogens.cif \<br>
| cif_cell_contents --use-attached-hydrogens
--assume-full-occupancies<br>
C254 H405 N14 O72 U8<br>
C254 H405 N14 O72 U8<br>
C254 H405 N14 O72 U8</font><br>
</blockquote>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">What would be you opinion on the
suggested interpretation of the structure? Adding all hydrogens
and marking the special position disorder would allow to generate
chemically uncontroversial models of all components in your
crystal, which would be IMHO of interest for chemists :)<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Also, please let me know if you need
more information about the COD deposition.<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">PS. What a nice cage structure you have
solved! I'm looking forward to see the paper that discusses this
structure!<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">[1] The uploaded C3ok.cif with the CIF
escape sequence instead of the Latin1 encoding. URL:
<a class="moz-txt-link-freetext" href="https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK.cif">https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK.cif</a>
[accessed 2023-02-19T19:07+02:00]</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">[2] The uploaded C3ok.cif with the CIF
escape sequence and reassigned disorder groups, marking disorder
around a special position. URL:
<a class="moz-txt-link-freetext" href="https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK-mark-disorder.cif">https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK-mark-disorder.cif</a>
[accessed 2023-02-19T19:32+02:00]<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">[3] The uploaded C3ok.cif with the CIF
escape sequence, reassigned disorder groups and attached hydrogens
mentioned for C15". URL:
<a class="moz-txt-link-freetext" href="https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK-mark-disorder-attached-hydrogens.cif">https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK-mark-disorder-attached-hydrogens.cif</a>
[accessed 2023-02-19T19:34+02:00]<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2023-02-18 09:55, Eduardo Carmelo
Escudero wrote:<br>
</div>
<blockquote type="cite"
cite="mid:HE1PR0602MB3387B75160929FDB11B56DF9A9A69@HE1PR0602MB3387.eurprd06.prod.outlook.com">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<style type="text/css" style="display:none;">P {margin-top:0;margin-bottom:0;}</style>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);" class="elementToProof">
<br>
</div>
<div class="elementToProof">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div>
<div style="font-family: Calibri, Arial, Helvetica,
sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
</div>
<div style="font-family:Tahoma; font-size:13px">
<p style="margin:0cm 0cm 0.0001pt"><b><span
style="font-size: 9pt; font-family: Tahoma; color:
rgb(64, 109, 119);" lang="EN-GB"></span></b></p>
<p style="margin: 0cm; font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(0, 0, 0); font-weight:
400; text-align: start; background-color: white;">
<b><span style="margin: 0px; padding: 0cm; border: 1pt
none windowtext; font-size: 9pt; font-family:
Tahoma, sans-serif; color: rgb(64, 109, 119);"
lang="EN-GB">Dr. Eduardo C. Escudero Adán</span></b><span
style="margin: 0px; font-size: 10pt; font-family:
Tahoma, sans-serif; color: black;" lang="ES"></span></p>
<p style="margin: 0cm; font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(0, 0, 0); font-weight:
400; text-align: start; background-color: white;">
<b><span style="margin: 0px; padding: 0cm; border: 1pt
none windowtext; font-size: 9pt; font-family:
Tahoma, sans-serif; color: black;" lang="EN-GB"><b
style="font-family:Calibri,
sans-serif;font-size:14.6667px"><span
style="margin: 0px; padding: 0cm; border: 1pt
none windowtext; font-size: 9pt; font-family:
Tahoma, sans-serif; color: black;" lang="EN-GB">Manager
of the </span></b>Characterization Technologies
Department </span></b><span style="margin: 0px;
font-size: 10pt; font-family: Tahoma, sans-serif;
color: black;" lang="ES"></span></p>
<p style="margin: 0cm; font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(0, 0, 0); font-weight:
400; text-align: start; background-color: white;">
<b><span style="margin: 0px; padding: 0cm; border: 1pt
none windowtext; font-size: 9pt; font-family:
Tahoma, sans-serif; color: black;" lang="EN-GB">Institute of
Chemical Research of Catalonia – ICIQ</span></b></p>
<p style="margin: 0cm; font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(0, 0, 0); font-weight:
400; text-align: start; background-color: white;">
<span style="margin: 0px; padding: 0cm; border: 1pt none
windowtext; color: black;" lang="ES">The Barcelona
Institute of Science and Technology - BIST</span><span
style="margin:0px;padding:0cm;border:1pt none
windowtext" lang="ES"></span></p>
<p style="margin: 0cm; font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(0, 0, 0); font-weight:
400; text-align: start; background-color: white;">
<span style="margin: 0px; padding: 0cm; border: 1pt none
windowtext; font-size: 9pt; font-family: Tahoma,
sans-serif; color: black;" lang="SV">Av. Països
Catalans 16 – 43007 Tarragona (Spain)</span><span
style="margin: 0px; font-size: 10pt; font-family:
Tahoma, sans-serif; color: black;" lang="ES"></span></p>
<p style="margin: 0cm; font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(0, 0, 0); font-weight:
400; text-align: start; background-color: white;">
<span style="margin: 0px; padding: 0cm; border: 1pt none
windowtext; font-size: 9pt; font-family: Tahoma,
sans-serif; color: black;" lang="EN-GB">Phone +34
977920238 – Ext. 122 Mobile +34 689 248 177</span></p>
<p style="margin:0cm 0cm 0.0001pt"><span
style="font-size:9pt; font-family:Tahoma" lang="EN-GB"></span></p>
<p style="margin:0cm 0cm 0.0001pt"><span
style="font-size:9pt; font-family:Tahoma" lang="FR"><a
href="mailto:eescudero@iciq.es"
moz-do-not-send="true" class="moz-txt-link-freetext">eescudero@iciq.es</a>
-
</span><span style="font-size:9pt; font-family:Tahoma"
lang="EN-GB"><a href="http://www.iciq.es/"
moz-do-not-send="true"><span style="" lang="FR">www.iciq.es</span></a> </span><span
style="font-size:9pt; font-family:Tahoma" lang="FR"><a
href="http://www.crysforma.es/"
moz-do-not-send="true"><span style="" lang="ES"></span></a></span></p>
<p class="MsoNormal" style="text-align:justify"><span
style="font-size:10pt; font-family:Tahoma" lang="FR"></span><span
style="font-size:8pt; font-family:Tahoma" lang="EN-GB">This
e-mail contains proprietary information whose content
can be protected by law. If you are not the intended
recipient, you may not use, disclose, distribute, copy
or print this e-mail. This confidential, personal and
not transferable e-mail is intended for the addressee
only and is legally protected. Any disclosure,
unauthorized use or forwarding, in whole or in part is
not permitted. If you are not the intended recipient
of this e-mail message and its contents, please notify
the sender immediately and delete this message and all
its attachments subsequently without reading or
record, in whole or in part. </span><span
style="font-size:8pt; font-family:Tahoma">Thank you</span><span
style="font-size:8pt; font-family:Tahoma" lang="EN-GB">.</span></p>
</div>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>De:</b> Eduardo
Carmelo Escudero <a class="moz-txt-link-rfc2396E" href="mailto:eescudero@ICIQ.ES"><eescudero@ICIQ.ES></a><br>
<b>Enviado:</b> martes, 14 de febrero de 2023 14:57<br>
<b>Para:</b> <a class="moz-txt-link-abbreviated" href="mailto:cod-bugs@ibt.lt">cod-bugs@ibt.lt</a> <a class="moz-txt-link-rfc2396E" href="mailto:cod-bugs@ibt.lt"><cod-bugs@ibt.lt></a><br>
<b>Cc:</b> Javier de Mendoza <a class="moz-txt-link-rfc2396E" href="mailto:jmendoza@ICIQ.ES"><jmendoza@ICIQ.ES></a><br>
<b>Asunto:</b> COD bug report e-mail</font>
<div> </div>
</div>
<style type="text/css" style="display:none">p
{margin-top:0;
margin-bottom:0}</style>
<div dir="ltr">
<div class="x_elementToProof"
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
</div>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span class="x_ContentPasted0" style="font-size:12pt;
color:black">Dear all, </span></p>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span style="font-size:12pt; color:black"> </span></p>
<p class="x_MsoNormal x_elementToProof" style="margin:0cm 0cm
0.0001pt; font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span class="x_ContentPasted0" style="font-size:12pt;
color:black">I am trying to upload a compressed single CIF
file
<span class="x_ContentPasted1" style="color:rgb(0,0,0);
background-color:rgb(255,255,255);
display:inline!important">
(see attached C3ok.zip file)<span class="x_ContentPasted1"> </span></span>but
the server does not allow it since the file size exceed the
size limit. </span></p>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span class="x_ContentPasted0" style="font-size:12pt;
color:black">How should I proceed to upload the CIF? </span></p>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span style="font-size:12pt; color:black"> </span></p>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span class="x_ContentPasted0" style="font-size:12pt;
color:black">Best wishes, </span></p>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span style="font-size:12pt; color:black"> </span></p>
<p class="x_MsoNormal" style="margin:0cm 0cm 0.0001pt;
font-size:11pt; font-family:Calibri,sans-serif;
background:white">
<span class="x_ContentPasted0" style="font-size:12pt;
color:black">Eduardo. </span></p>
<div class="x_elementToProof"
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
</div>
<div class="x_elementToProof">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div id="x_Signature">
<div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
</div>
<div style="font-family:Tahoma; font-size:13px">
<p style="margin:0cm 0cm 0.0001pt"><b><span
style="font-size:9pt; font-family:Tahoma;
color:rgb(64,109,119)" lang="EN-GB"></span></b></p>
<p style="margin:0cm; font-size:11pt;
font-family:Calibri,sans-serif; color:rgb(0,0,0);
font-weight:400; text-align:start;
background-color:white">
<b><span style="margin:0px; padding:0cm; border:1pt
none windowtext; font-size:9pt;
font-family:Tahoma,sans-serif;
color:rgb(64,109,119)" lang="EN-GB">Dr. Eduardo C.
Escudero Adán</span></b><span style="margin:0px;
font-size:10pt; font-family:Tahoma,sans-serif;
color:black" lang="ES"></span></p>
<p style="margin:0cm; font-size:11pt;
font-family:Calibri,sans-serif; color:rgb(0,0,0);
font-weight:400; text-align:start;
background-color:white">
<b><span style="margin:0px; padding:0cm; border:1pt
none windowtext; font-size:9pt;
font-family:Tahoma,sans-serif; color:black"
lang="EN-GB"><b
style="font-family:Calibri,sans-serif;
font-size:14.6667px"><span style="margin:0px;
padding:0cm; border:1pt none windowtext;
font-size:9pt; font-family:Tahoma,sans-serif;
color:black" lang="EN-GB">Manager of the </span></b>Characterization
Technologies Department </span></b><span
style="margin:0px; font-size:10pt;
font-family:Tahoma,sans-serif; color:black"
lang="ES"></span></p>
<p style="margin:0cm; font-size:11pt;
font-family:Calibri,sans-serif; color:rgb(0,0,0);
font-weight:400; text-align:start;
background-color:white">
<b><span style="margin:0px; padding:0cm; border:1pt
none windowtext; font-size:9pt;
font-family:Tahoma,sans-serif; color:black"
lang="EN-GB">Institute of Chemical Research of
Catalonia – ICIQ</span></b></p>
<p style="margin:0cm; font-size:11pt;
font-family:Calibri,sans-serif; color:rgb(0,0,0);
font-weight:400; text-align:start;
background-color:white">
<span style="margin:0px; padding:0cm; border:1pt none
windowtext; color:black" lang="ES">The Barcelona
Institute of Science and Technology - BIST</span><span
style="margin:0px; padding:0cm; border:1pt none
windowtext" lang="ES"></span></p>
<p style="margin:0cm; font-size:11pt;
font-family:Calibri,sans-serif; color:rgb(0,0,0);
font-weight:400; text-align:start;
background-color:white">
<span style="margin:0px; padding:0cm; border:1pt none
windowtext; font-size:9pt;
font-family:Tahoma,sans-serif; color:black"
lang="SV">Av. Països Catalans 16 – 43007 Tarragona
(Spain)</span><span style="margin:0px;
font-size:10pt; font-family:Tahoma,sans-serif;
color:black" lang="ES"></span></p>
<p style="margin:0cm; font-size:11pt;
font-family:Calibri,sans-serif; color:rgb(0,0,0);
font-weight:400; text-align:start;
background-color:white">
<span style="margin:0px; padding:0cm; border:1pt none
windowtext; font-size:9pt;
font-family:Tahoma,sans-serif; color:black"
lang="EN-GB">Phone +34 977920238 – Ext. 122 Mobile
+34 689 248 177</span></p>
<p style="margin:0cm 0cm 0.0001pt"><span
style="font-size:9pt; font-family:Tahoma"
lang="EN-GB"></span></p>
<p style="margin:0cm 0cm 0.0001pt"><span
style="font-size:9pt; font-family:Tahoma" lang="FR"><a
href="mailto:eescudero@iciq.es"
moz-do-not-send="true"
class="moz-txt-link-freetext">eescudero@iciq.es</a>
-
</span><span style="font-size:9pt; font-family:Tahoma"
lang="EN-GB"><a href="http://www.iciq.es/"
moz-do-not-send="true"><span style="" lang="FR">www.iciq.es</span></a> </span><span
style="font-size:9pt; font-family:Tahoma" lang="FR"><a
href="http://www.crysforma.es/"
moz-do-not-send="true"><span style="" lang="ES"></span></a></span></p>
<p class="x_MsoNormal" style="text-align:justify"><span
style="font-size:10pt; font-family:Tahoma" lang="FR"></span><span
style="font-size:8pt; font-family:Tahoma"
lang="EN-GB">This e-mail contains proprietary
information whose content can be protected by law.
If you are not the intended recipient, you may not
use, disclose, distribute, copy or print this
e-mail. This confidential, personal and not
transferable e-mail is intended for the addressee
only and is legally protected. Any disclosure,
unauthorized use or forwarding, in whole or in part
is not permitted. If you are not the intended
recipient of this e-mail message and its contents,
please notify the sender immediately and delete this
message and all its attachments subsequently without
reading or record, in whole or in part. </span><span
style="font-size:8pt; font-family:Tahoma">Thank you</span><span
style="font-size:8pt; font-family:Tahoma"
lang="EN-GB">.</span></p>
</div>
</div>
</div>
</div>
</div>
<br>
-- <br>
This message has been scanned for viruses and
<br>
dangerous content by
<a href="http://www.mailscanner.info/" moz-do-not-send="true"><b>MailScanner</b></a>,
and is
<br>
believed to be clean.
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Cod-bugs mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Cod-bugs@lists.crystallography.net">Cod-bugs@lists.crystallography.net</a>
<a class="moz-txt-link-freetext" href="http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs">http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs</a>
</pre>
</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>
</body>
</html>