[Cod-bugs] RV: COD bug report e-mail

Wed Mar 1 11:14:15 EET 2023

Dear Salius,

Thank you very much for your inestimable help and detailed comments. (Sorry for may late response but I was out of the office).
I have reorganized the disordered fragments as you specified to avoid any misleading interpretation of the structure with the COD software. In the same manner, Hs atoms have been added to C15” as you correctly suggest.
The deposition was successful this time despite the CIF size. (3000433)

Thank you again for your help.

Best wishes,

Eduardo.

From: Saulius Gražulis <grazulis at ibt.lt>
Sent: Sunday, February 19, 2023 6:55 PM
To: Eduardo Carmelo Escudero <eescudero at ICIQ.ES>; cod-bugs at ibt.lt
Cc: Javier de Mendoza <jmendoza at ICIQ.ES>
Subject: Re: [Cod-bugs] RV: COD bug report e-mail

Dear Eduardo,

thank you very much for your e-mail, for offering your work for COD, and my big apologies for not responding earlier.

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.

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:

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;

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.

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:

3a) Adding the hydrogens model explicitly and re-running SHELX analysis to get the (slightly) updated statistics (R-factors et al.);

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].

The change suggested in (3) would add one hydrogen to your structure (2 half occupied H sites), and thus change the formula from 'C254 H404 N14 O72 U8' to 'C254 H405 N14 O72 U8'. The latter formula, however, would agree with individual formulae of each disordered assembly collection:

saulius at tasmanijos-velnias COD-deposition-big-file/ $ cif_molecule --one-datablock C3ok-charset-OK-mark-disorder-attached-hydrogens.cif \
    | cif_cell_contents --use-attached-hydrogens --assume-full-occupancies
C254 H405 N14 O72 U8
C254 H405 N14 O72 U8
C254 H405 N14 O72 U8

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 :)

Also, please let me know if you need more information about the COD deposition.

Sincerely yours,
Saulius

PS. What a nice cage structure you have solved! I'm looking forward to see the paper that discusses this structure!

Refs.:

[1] The uploaded C3ok.cif with the CIF escape sequence instead of the Latin1 encoding. URL: https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK.cif [accessed 2023-02-19T19:07+02:00]

[2] The uploaded C3ok.cif with the CIF escape sequence and reassigned disorder groups, marking disorder around a special position. URL: https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK-mark-disorder.cif [accessed 2023-02-19T19:32+02:00]

[3] The uploaded C3ok.cif with the CIF escape sequence, reassigned disorder groups and attached hydrogens mentioned for C15". URL: https://saulius-grazulis.lt/~saulius/.cb3871ea07a849222ed6e0091b57dc56a523bef4/C3ok-charset-OK-mark-disorder-attached-hydrogens.cif [accessed 2023-02-19T19:34+02:00]

On 2023-02-18 09:55, Eduardo Carmelo Escudero wrote:

Dr. Eduardo C. Escudero Adán

Manager of the Characterization Technologies Department

Institute of Chemical Research of Catalonia – ICIQ

The Barcelona Institute of Science and Technology - BIST

Av. Països Catalans 16 – 43007 Tarragona (Spain)

Phone +34 977920238 – Ext. 122   Mobile +34 689 248 177

eescudero at iciq.es<mailto:eescudero at iciq.es> - www.iciq.es<http://www.iciq.es/>
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. Thank you.
________________________________
De: Eduardo Carmelo Escudero <eescudero at ICIQ.ES><mailto:eescudero at ICIQ.ES>
Enviado: martes, 14 de febrero de 2023 14:57
Para: cod-bugs at ibt.lt<mailto:cod-bugs at ibt.lt> <cod-bugs at ibt.lt><mailto:cod-bugs at ibt.lt>
Cc: Javier de Mendoza <jmendoza at ICIQ.ES><mailto:jmendoza at ICIQ.ES>
Asunto: COD bug report e-mail

Dear all,

I am trying to upload a compressed single CIF file (see attached C3ok.zip file) but the server does not allow it since the file size exceed the size limit.

How should I proceed to upload the CIF?

Best wishes,

Eduardo.

Dr. Eduardo C. Escudero Adán

Manager of the Characterization Technologies Department

Institute of Chemical Research of Catalonia – ICIQ

The Barcelona Institute of Science and Technology - BIST

Av. Països Catalans 16 – 43007 Tarragona (Spain)

Phone +34 977920238 – Ext. 122   Mobile +34 689 248 177

eescudero at iciq.es<mailto:eescudero at iciq.es> - www.iciq.es<http://www.iciq.es/>

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. Thank you.

--
This message has been scanned for viruses and
dangerous content by MailScanner<http://www.mailscanner.info/>, and is
believed to be clean.

_______________________________________________

Cod-bugs mailing list

Cod-bugs at lists.crystallography.net<mailto:Cod-bugs at lists.crystallography.net>

http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs

--

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

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20230301/8fa88313/attachment-0001.htm>