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<div class="moz-cite-prefix">Dear Dr. Sakurabayashi,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">I have inserted the data items form you
mail (below) into the on-hold COD entry 3000497.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">You may want to verify at the
<a class="moz-txt-link-freetext" href="https://www.crystallography.net/cod/manage_depositions.php">https://www.crystallography.net/cod/manage_depositions.php</a> Web
page (after the login) that the changes correspond to you original
intended antry.</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">Sincerely yours,<br>
Saulius<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2024-04-24 09:38, Saulius Gražulis
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:3fa9a062-4aca-455a-9894-b11c07d73aca@ibt.lt">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div class="moz-cite-prefix">Dear dr. Sakurabayashi,</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">thank you for your message. I'm very
glad that your deposition worked!<br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 2024-04-24 04:01, <a
class="moz-txt-link-abbreviated moz-txt-link-freetext"
href="mailto:sakurabayashi26@sanken.osaka-u.ac.jp"
moz-do-not-send="true">sakurabayashi26@sanken.osaka-u.ac.jp</a>
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp">
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<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US">Dear Dr. Saulius,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">Thank you for the reply.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">>1. please comment out the
'_refine_ls_R_factor_gt' and the
'_refine_ls_wR_factor_ref' lines (data >items) in
>you submitted file; you can do this in the COD
deposition site editor. Please save these >lines on you
>computer in a separate file;<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">I just deposited the cif file with the two
lines above commented out.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">Deposition seems to have worked.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">>2. your submission should be then ready
for deposition ("green"). Please deposit it and send us:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">> a) the COD ID of the deposited
structure;<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">> b) the saved '_refine_ls_R_factor_gt'
and the '_refine_ls_wR_factor_ref' lines (data items;<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">The COD ID is 3000497.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">Those two lines are shown below;<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:42.0pt"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">_refine_ls_R_factor_gt 0.2149<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:42.0pt"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US">_refine_ls_wR_factor_ref 0.5835</span></p>
</div>
</blockquote>
<blockquote type="cite"
cite="mid:004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp">
<div class="WordSection1">
<p class="MsoNormal" style="text-indent:42.0pt"><span
style="font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Arial",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoPlainText"><span lang="EN-US">If necessary,
please add the below comment as the reason of errors.<o:p></o:p></span></p>
<p class="MsoPlainText" style="text-indent:42.0pt"><span
lang="EN-US">This is a MicroED structure refined only
kinematically.<o:p></o:p></span></p>
<p class="MsoPlainText" style="text-indent:42.0pt"><span
lang="EN-US">Thus, traditional X-ray crystallography
thresholds are not adequate.</span></p>
</div>
</blockquote>
<p>Excellent! I'll insert the values into your structure in the
'on-hold' repository. The values will be there when the
structure is released.</p>
<span lang="EN-US"><o:p></o:p></span>
<blockquote type="cite"
cite="mid:004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp">
<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US">If there are still any deficiencies regarding
depositions, I would appreciate it if you could let me
know.</span></p>
</div>
</blockquote>
<p>I'll let you know but for now everything seems OK!</p>
<p>Sincerely yours,<br>
Saulius<br>
<br>
</p>
<blockquote type="cite"
cite="mid:004d01da95e2$e96d68a0$bc4839e0$@sanken.osaka-u.ac.jp">
<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US">Shuhei Sakurabayashi<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
<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
href="mailto:grazulis@ibt.lt" moz-do-not-send="true"
class="moz-txt-link-freetext">grazulis@ibt.lt</a> <br>
<b>Sent:</b> Tuesday, April 23, 2024 3:04 PM<br>
<b>To:</b> <a
href="mailto:cod-bugs@lists.crystallography.net"
moz-do-not-send="true" class="moz-txt-link-freetext">cod-bugs@lists.crystallography.net</a>;
<a href="mailto:sakurabayashi26@sanken.osaka-u.ac.jp"
moz-do-not-send="true" class="moz-txt-link-freetext">sakurabayashi26@sanken.osaka-u.ac.jp</a><br>
<b>Subject:</b> Re: [Cod-bugs] Fwd: Cod-bugs post from <a
href="mailto:sakurabayashi26@sanken.osaka-u.ac.jp"
moz-do-not-send="true" class="moz-txt-link-freetext">sakurabayashi26@sanken.osaka-u.ac.jp</a>
requires approval<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Dear dr. Sakurabayashi<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">thank you for
depositing your data to the COD!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Indeed, we should
relax Rf requirements for the MicroED structures, but for
now, please proceed as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">1. please comment out
the '_refine_ls_R_factor_gt' and the
'_refine_ls_wR_factor_ref' lines (data items) in you
submitted file; you can do this in the COD deposition site
editor. Please save these lines on you computer in a
separate file;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">2. your submission
should be then ready for deposition ("green"). Please
deposit it and send us:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> a) the COD ID of
the deposited structure;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> b) the saved
'_refine_ls_R_factor_gt' and the
'_refine_ls_wR_factor_ref' lines (data items;<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">We will reinsert them
into your deposited file with the appropriate comment. You
should also be able to reinsert them in the COD data
editing Web window if you would like to do so.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">HTH,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Sincerely yours,<br>
Saulius<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Yu Gothic",sans-serif"
lang="EN-US"><o:p> </o:p></span></p>
</div>
<br>
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<p><br>
</p>
<pre class="moz-signature" cols="72">--
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366
</pre>
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