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<div class="moz-cite-prefix">Dear Dr. Toshiyuki,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you for the e-mail! I'll insert
the ...R_factor_... data names into you submitted CIFs where
necessary.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">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 class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">The '_cod_related_entry_[]' at the
moment looks like this:</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">
<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 class="moz-cite-prefix">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 class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">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 class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">BTW, will your your colleagues be at
the ECM34? It would be nice to meet and talk in person :)<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Regards,<br>
Saulius<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2024-08-02 08:04, Toshiyuki Sasaki
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:02c501dae499$85a9adf0$90fd09d0$@spring8.or.jp">
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Dear Dr. Saulius Gražulis,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">I have uploaded crystal structures with some
errors solved by MicroED to COD.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
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.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Deposited data and related information<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">3000560: merged 13 crystals <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Removed lines for the deposition<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">_refine_ls_wR_factor_ref 0.4090<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">3000561: merged 9 crystals<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Removed lines for the deposition<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">_refine_ls_R_factor_gt 0.1540<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">_refine_ls_wR_factor_ref 0.3972 <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Regarding EM images, what can I do?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
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:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">“<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Thank you for your cooperation.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Toshiyuki<o:p></o:p></span></p>
<div>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">**************************************************************<o:p></o:p></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D">公益財団法人高輝度光科学研究センター<span
lang="EN-US"><o:p></o:p></span></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">(</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:black;background:white" lang="EN-US">Japan
Synchrotron Radiation Research Institute</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US"> (</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">JASRI))<o:p></o:p></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D">回折・散乱推進室<span lang="EN-US"> (</span></span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">Diffraction and
Scattering Division</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">)</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D">テニュアトラック研究員<span lang="EN-US">
(</span></span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">Tenure-track
researcher</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">)</span><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D">佐々木 俊之<span lang="EN-US"> (Dr.
Toshiyuki Sasaki)<o:p></o:p></span></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">TEL:
0791-58-0802(3430)<o:p></o:p></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:black;background:white">〒<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"><o:p></o:p></span></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:black;background:white" lang="EN-US">(1-1-1,
Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 Japan)<o:p></o:p></span></p>
<p class="MsoNormal"
style="text-align:justify;text-justify:inter-ideograph"><span
style="font-size:10.5pt;font-family:"游ゴシック
Light";color:#1F497D" lang="EN-US">**************************************************************<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0mm
0mm 0mm 4.0pt">
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0mm 0mm 0mm">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US"> Saulius Gražulis
[<a class="moz-txt-link-freetext" href="mailto:grazulis@ibt.lt">mailto:grazulis@ibt.lt</a>] <br>
<b>Sent:</b> Thursday, June 27, 2024 3:18 PM<br>
<b>To:</b> Toshiyuki Sasaki
<a class="moz-txt-link-rfc2396E" href="mailto:toshiyuki.sasaki@spring8.or.jp"><toshiyuki.sasaki@spring8.or.jp></a><br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:cod-bugs@lists.crystallography.net">cod-bugs@lists.crystallography.net</a><br>
<b>Subject:</b> Re: COD Data registration<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-US">On 2024-06-27 09:14,
Toshiyuki Sasaki wrote:<o:p></o:p></span></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">Finally our paper was published on Journal
of Materials Chemistry C.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">The deposited CIF files (3000450, 3000451)
were just updated by including publication information.</span><span
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">In addition, I give you DOI of XRDa of
these structures as I promised.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:游ゴシック;color:#1F497D"
lang="EN-US">3000450, 3000451: </span><span
lang="EN-US"><a
href="https://doi.org/10.51093/xrd-00142"
target="_blank" moz-do-not-send="true"><span
style="font-size:14.5pt;font-family:"Verdana",sans-serif">10.51093/xrd-00142</span></a><o:p></o:p></span></p>
</blockquote>
<p><span lang="EN-US">Thanks a lot for your update, and
congratulations with your publication!<o:p></o:p></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.<o:p></o:p></span></p>
<p><span lang="EN-US">Sincerely yours,<br>
Saulius<o:p></o:p></span></p>
<pre><span lang="EN-US">-- <o:p></o:p></span></pre>
<pre><span lang="EN-US">Dr. Saulius Gražulis<o:p></o:p></span></pre>
<pre><span lang="EN-US">Vilnius University Institute of Biotechnology, Saulėtekio al. 7<o:p></o:p></span></pre>
<pre><span lang="EN-US">LT-10257 Vilnius, Lietuva (Lithuania)<o:p></o:p></span></pre>
<pre><span lang="EN-US">mobile: (+370-684)-49802, (+370-614)-36366<o:p></o:p></span></pre>
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<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
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