<div dir="ltr">Dear Dr. Saulius Gražulis<div><br></div><div>Sorry for the lack of information.<br><div><blockquote type="cite"><span class="gmail-im" style="color:rgb(80,0,80)"><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">Deposited data and related information<u></u><u></u></span></p></span><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">3000560: </span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">taca-ina-meno2_fill.cif</span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">data_taca-ina-meno2</span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">merged 13 crystals<u></u><u></u></span></p><span class="gmail-im" style="color:rgb(80,0,80)"><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">Removed lines for the deposition<u></u><u></u></span></p></span><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">_refine_ls_wR_factor_ref 0.4090<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">3000561:</span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">TACA-INA-Toluene_fill.cif</span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">data_taca-ina-toluene</span></p><p class="MsoNormal"><span style="color:rgb(31,73,125);font-family:游ゴシック;font-size:11pt">merged 9 crystals</span><br></p><span class="gmail-im" style="color:rgb(80,0,80)"><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">Removed lines for the deposition<u></u><u></u></span></p></span><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">_refine_ls_R_factor_gt 0.1540<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)">_refine_ls_wR_factor_ref 0.3972</span></p></blockquote>>
BTW, will your your colleagues be at the ECM34? It would be nice to meet and talk in person :)<br class="gmail-Apple-interchange-newline">I will not be there and I don't know whether my collaborators join the ECM34 or not.</div></div><div>Anyway, I mentioned about you and if someone will attend the ECM34, he will contact you :)</div><div><br></div><div>Best regards,</div><div><br></div><div>Toshiyuki Sasaki</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2024年8月2日(金) 18:02 Saulius Gražulis <<a href="mailto:grazulis@ibt.lt">grazulis@ibt.lt</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>Dear Dr. Toshiyuki,</div>
<div><br>
</div>
<div>thank you for the e-mail! I'll insert
the ...R_factor_... data names into you submitted CIFs where
necessary.</div>
<div><br>
</div>
<div>Regarding the references to the image
locations, there are two mechanisms that that we consider using.
One is the IUCr suggestion by Brian McMahon announced at the IUCr
Congress last year. Another is the intrinsic COD mechanism using
the '_cod_related_entry_[]' category. Both requite certain update
of the COD infrastructure, which I plan to do, hopefully, before
leaving to the ECM34 this month.</div>
<div><br>
</div>
<div>The '_cod_related_entry_[]' at the
moment looks like this:</div>
<div><br>
</div>
<div>
<blockquote type="cite"><font face="monospace">saulius@tasmanijos-velnias
cod-tools/ $ tail -5
/home/saulius/struct/cod/current/cif/9/01/51/9015157.cif<br>
loop_<br>
_cod_related_entry_id<br>
_cod_related_entry_database<br>
_cod_related_entry_code<br>
1 AMCSD 0018609</font><br>
</blockquote>
</div>
<div>In a similar way, we could use an
external database, say XRDA [1], and gibe a link to the database's
record (unique ID).</div>
<div><br>
</div>
<div>For this I need to make an additional
SQL table in the COD, xrda_x_cod, and update the COD deposition
scripts so that they populate that new table. It is not a large
work, I just need to find two free days to implement and test this
:)<br>
</div>
<div><br>
</div>
<div>BTW, will your your colleagues be at
the ECM34? It would be nice to meet and talk in person :)<br>
</div>
<div><br>
</div>
<div>Regards,<br>
Saulius<br>
</div>
<div><br>
</div>
<div>On 2024-08-02 08:04, Toshiyuki Sasaki
wrote:<br>
</div>
<blockquote type="cite">
<div>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Dear Dr. Saulius Gražulis,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">I have uploaded crystal structures with some
errors solved by MicroED to COD.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">By following the previous procedures (remove
lines and give you information about the errors etc.), I
would like you to handle the data properly.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Deposited data and related information<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">3000560: merged 13 crystals <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Removed lines for the deposition<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">_refine_ls_wR_factor_ref 0.4090<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">3000561: merged 9 crystals<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Removed lines for the deposition<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">_refine_ls_R_factor_gt 0.1540<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">_refine_ls_wR_factor_ref 0.3972 <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Regarding EM images, what can I do?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">“</span><span lang="EN-US">I'll come back to
your shortly with a suggested update of your data files.</span><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">“<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Thank you for your cooperation.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Best regards,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US"> <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Toshiyuki<u></u><u></u></span></p>
<div>
<p class="MsoNormal" style="text-align:justify"><span lang="EN-US">**************************************************************<u></u><u></u></span></p>
<p class="MsoNormal" style="text-align:justify"><span>公益財団法人高輝度光科学研究センター<span lang="EN-US"><u></u><u></u></span></span></p>
<p class="MsoNormal" style="text-align:justify"><span lang="EN-US">(</span><span lang="EN-US">Japan
Synchrotron Radiation Research Institute</span><span lang="EN-US"> (</span><span lang="EN-US">JASRI))<u></u><u></u></span></p>
<p class="MsoNormal" style="text-align:justify"><span>回折・散乱推進室<span lang="EN-US"> (</span></span><span lang="EN-US">Diffraction and
Scattering Division</span><span lang="EN-US">)</span><span lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal" style="text-align:justify"><span>テニュアトラック研究員<span lang="EN-US">
(</span></span><span lang="EN-US">Tenure-track
researcher</span><span lang="EN-US">)</span><span lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal" style="text-align:justify"><span>佐々木 俊之<span lang="EN-US"> (Dr.
Toshiyuki Sasaki)<u></u><u></u></span></span></p>
<p class="MsoNormal" style="text-align:justify"><span lang="EN-US">TEL:
0791-58-0802(3430)<u></u><u></u></span></p>
<p class="MsoNormal" style="text-align:justify"><span>〒<span lang="EN-US">679-5198</span> 兵庫県佐用郡佐用町光都<span lang="EN-US">1</span>丁目<span lang="EN-US">1</span>番<span lang="EN-US">1</span>号<span lang="EN-US"><u></u><u></u></span></span></p>
<p class="MsoNormal" style="text-align:justify"><span lang="EN-US">(1-1-1,
Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 Japan)<u></u><u></u></span></p>
<p class="MsoNormal" style="text-align:justify"><span lang="EN-US">**************************************************************<u></u><u></u></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US"><u></u> <u></u></span></p>
<div style="border-top:none;border-right:none;border-bottom:none;border-left:1.5pt solid blue;padding:0mm 0mm 0mm 4pt">
<div>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(225,225,225);padding:3pt 0mm 0mm">
<p class="MsoNormal"><b><span style="font-size:11pt;font-family:Calibri,sans-serif" lang="EN-US">From:</span></b><span style="font-size:11pt;font-family:Calibri,sans-serif" lang="EN-US"> Saulius Gražulis
[<a href="mailto:grazulis@ibt.lt" target="_blank">mailto:grazulis@ibt.lt</a>] <br>
<b>Sent:</b> Thursday, June 27, 2024 3:18 PM<br>
<b>To:</b> Toshiyuki Sasaki
<a href="mailto:toshiyuki.sasaki@spring8.or.jp" target="_blank"><toshiyuki.sasaki@spring8.or.jp></a><br>
<b>Cc:</b> <a href="mailto:cod-bugs@lists.crystallography.net" target="_blank">cod-bugs@lists.crystallography.net</a><br>
<b>Subject:</b> Re: COD Data registration<u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US">On 2024-06-27 09:14,
Toshiyuki Sasaki wrote:<u></u><u></u></span></p>
</div>
<blockquote style="margin-top:5pt;margin-bottom:5pt">
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">Finally our paper was published on Journal
of Materials Chemistry C.</span><span lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">The deposited CIF files (3000450, 3000451)
were just updated by including publication information.</span><span lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">In addition, I give you DOI of XRDa of
these structures as I promised.</span><span lang="EN-US"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:游ゴシック;color:rgb(31,73,125)" lang="EN-US">3000450, 3000451: </span><span lang="EN-US"><a href="https://doi.org/10.51093/xrd-00142" target="_blank"><span style="font-size:14.5pt;font-family:Verdana,sans-serif">10.51093/xrd-00142</span></a><u></u><u></u></span></p>
</blockquote>
<p><span lang="EN-US">Thanks a lot for your update, and
congratulations with your publication!<u></u><u></u></span></p>
<p><span lang="EN-US">I'll have a look at the data. Also, I
remember that your have published the links to original EM
images; it would be great to include these links into the
COD files as well. We have recently developed a mechanism
how this can be done,; I'll come back to your shortly with
a suggested update of your data files.<u></u><u></u></span></p>
<p><span lang="EN-US">Sincerely yours,<br>
Saulius<u></u><u></u></span></p>
<pre><span lang="EN-US">-- <u></u><u></u></span></pre>
<pre><span lang="EN-US">Dr. Saulius Gražulis<u></u><u></u></span></pre>
<pre><span lang="EN-US">Vilnius University Institute of Biotechnology, Saulėtekio al. 7<u></u><u></u></span></pre>
<pre><span lang="EN-US">LT-10257 Vilnius, Lietuva (Lithuania)<u></u><u></u></span></pre>
<pre><span lang="EN-US">mobile: (+370-684)-49802, (+370-614)-36366<u></u><u></u></span></pre>
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<pre 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
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