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<div class="moz-cite-prefix">Dear Dr. <span
style="font-family:"游ゴシック Light""><span lang="EN-US">Sasaki,</span></span></div>
<div class="moz-cite-prefix"><span style="font-family:"游ゴシック
Light""><span lang="EN-US"><br>
</span></span></div>
<div class="moz-cite-prefix"><span style="font-family:"游ゴシック
Light""><span lang="EN-US">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.<br>
</span></span></div>
<div class="moz-cite-prefix"><span style="font-family:"游ゴシック
Light""><span lang="EN-US"><br>
</span></span></div>
<div class="moz-cite-prefix">On 2023-05-12 03:14, Toshiyuki Sasaki
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:00e601d98466$b9f40d10$2ddc2730$@spring8.or.jp">
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">I’m
Toshiyuki Sasaki, a researcher in Japan Synchrotron Radiation
Research Institute.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Before
publishing a paper, I want to upload CIF files to COD.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">What
can I do for the problem?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">The
paper is almost accepted with the CIF files.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p></o:p></span></p>
</blockquote>
<p>May I suggest two options for your deposition:</p>
<p>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.</p>
<p>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.</p>
<p>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.<br>
</p>
<p>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.<br>
</p>
<p>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.</p>
<p>Please let us know what is your preferred way to proceed.<br>
</p>
<p>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.</p>
<p>The _refine_ls_R_factor_gt and _refine_ls_wR_factor_ref, however,
are somewhat high, even for electron diffraction studies. <br>
</p>
<p>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?</p>
<p>I also see that there are large values reported for the symmetry
equivalent reflection agreement:</p>
<p>
<blockquote type="cite"><font face="monospace">_diffrn_reflns_av_R_equivalents
0.8897<br>
_diffrn_reflns_av_unetI/netI 0.3546</font><br>
</blockquote>
</p>
<p>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?<br>
</p>
<p>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?<br>
</p>
<p>Sicnerely yours,<br>
Saulius</p>
<p>[1] CheckCIF, a service of the IUCr (2023). URL:
<a class="moz-txt-link-freetext" href="https://checkcif.iucr.org/">https://checkcif.iucr.org/</a> [accessed 2023-05-13T13:15+03:00]<br>
</p>
<pre class="moz-signature" cols="72">--
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
</pre>
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