[Cod-bugs] Data registration

[Saulius Gražulis]

Dear Dr. Sasaki,

thank you very much for your inquire and for entrusting your data to
Crystallography Open Database! Below, I'll give you suggestions how to
solve your data deposition problem and some thoughts on the parameters
of the CIF.

On 2023-05-12 03:14, Toshiyuki Sasaki wrote:
>
> I’m Toshiyuki Sasaki, a researcher in Japan Synchrotron Radiation
> Research Institute.
>
> Before publishing a paper, I want to upload CIF files to COD.
>
> However, due to the warnings of “data item ‘_refine_ls_R_factor_gt’
> and ‘_refine_ls_wR_factor_ref’”, I could not deposit the files.
>
> What can I do for the problem?
>
> The paper is almost accepted with the CIF files.
>
May I suggest two options for your deposition:

a) you temporarily remove the  ‘_refine_ls_R_factor_gt’ and
‘_refine_ls_wR_factor_ref’ data items from the CIF (best of all, you use
the "Edit" button in the COD deposition Web site) and commit. The system
should allow the deposition. After that you send us the two removed
lines in a separate e-mail, along with the COD ID that your structure
has been assigned, and we will reinsert the data into your deposited
structure as a part of the data curation process.

b) you send us the original CIF, together with the rest of the metadata
(the complete author list, on-hold period, intended journal, etc.), and
we deposit it for you directly to the low-level database, and send you
the assigned COD ID.

c) if your uploaded file is the "OLN-SUCA.cif" as I see from the COD
server logs, you can send us a checksum (MD5, SHA1 or SHA256) of your
original uploaded file, together with the metadata (the complete author
list, on-hold period, intended journal, etc.), and confirm that your
uploaded this file for deposition; we will then extract the file from
the COD server logs and finish the deposition for you, sending the COD
ID ASAP.

Of course we assure that your data will be confidential before the
release date that you will specify, or before the publication of your
paper, whichever comes first.

The (a) route would be the fastest way to obtain the COD ID and to
proceed with your publication, but it will require you to edit the file,
preferably using the COD deposition Web site. In case of (b) or (c),
we'll do our best to deposit the structure as soon as possible, but it
may a working day or two to process.

Please let us know what is your preferred way to proceed.

I have several questions regarding your structure. To troubleshoot your
question, I have allowed myself to look into your crude deposited files
on the COD server. It is a very interesting case of electron
diffraction, as I understood from the data. The structure seems very
reasonable, with bond lengths and angles (as I can judge from the visual
inspection on the computer graphics) comfortable within expected limits,
and thermal ellipsoids close to isotropicity and with no unexpected
features.

The _refine_ls_R_factor_gt and _refine_ls_wR_factor_ref, however, are
somewhat high, even for electron diffraction studies.

Moreover, I have noticed that the _exptl_absorpt_coefficient_mu is zero,
and the remaining absorption correction parameters are not specified. I
see that very few of the electron diffraction studies reported in the
COD use absorption correction, but if it is technically possible to
apply it, maybe the final refinement R-factors will get lower?

I also see that there are large values reported for the symmetry
equivalent reflection agreement:

> _diffrn_reflns_av_R_equivalents    0.8897
> _diffrn_reflns_av_unetI/netI       0.3546

The COD min / avg / max values are 0.0661 / 0.218177 (sample σ = 0.099)
/ 0.4322 for _diffrn_reflns_av_R_equivalents and 0.0007 / 0.141944
(sample σ = 0.120) / 0.5071 for _diffrn_reflns_av_unetI/netI; thus the
values in your file seem quite high compared to what we see in the COD
(for the 35 structures explicitly reported as electron diffraction
studies by setting 'radiation' column to 'electron'), the
_diffrn_reflns_av_R_equivalents is beyond 5*σ. Could it  be that
applying absorption correction would decrease these statistics as well?

I did not use the CheckCIF [1] tool to avoid breaking confidentiality of
your structure, but it would be interesting if your could get a CheckCIF
/ PLATO reports on your structure. Are there any Level A alerts?

Sicnerely yours,
Saulius

[1] CheckCIF, a service of the IUCr (2023). URL:
https://checkcif.iucr.org/ [accessed 2023-05-13T13:15+03:00]

-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366


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