[Cod-bugs] RV: COD bug report e-mail
Saulius Gražulis
grazulis at ibt.lt
Sun Feb 19 19:55:29 EET 2023
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 - www.iciq.es <http://www.iciq.es/>
> <http://www.crysforma.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
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> 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>
> *Enviado:* martes, 14 de febrero de 2023 14:57
> *Para:* cod-bugs at ibt.lt <cod-bugs at ibt.lt>
> *Cc:* Javier de Mendoza <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 - www.iciq.es <http://www.iciq.es/>
> <http://www.crysforma.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
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--
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
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-- Hydrogen atoms H14P, H14Q, H14R, H14S should be long to disorder
assembly C, groups 1 (H14P + H14Q) and 2 (H14R + H14S),
respectively, to be adjoined to the corresponding C14F atom in the
necessary configurations (I have distributed the disorder groups so
that each group has hydrogen atoms with the angles closest to the
tetrahedral configuration);
-- Atom C15" lacks its methylene hydrogen atoms (maybe they can be
modelled?);
-- Atoms in the disorder assembly "I" (group 2) are instead assigned
to the disorder assembly "H" (group 2), so that they are perceived
as alternatives of the same assembly "H", disorder group 1. This
means that the group "H" represents two alternative conformations
(groups 1 and 2) of the same N,N-Dimethylformamide moiety;
-- Atoms H911 and H921 are assigned to the disorder assembly "F",
group 1 (together with the atom C10I), and the atoms H912 and H922
are assigned to the group 2 of the same assembly (together with the
atom C10'), to maintain two alternative conformations of the
tetrabutylammonium moiety;
-- Reassigning disorder assembly "G" groups to analogous disorder
assembly "F" groups, so that their perceived "movement" is
correlated and no steric clashes arise when generating
alternatives.
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