<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Aptos;
panose-1:2 11 0 4 2 2 2 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Aptos",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#467886;
text-decoration:underline;}
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
margin-top:0cm;
margin-right:0cm;
margin-bottom:0cm;
margin-left:36.0pt;
font-size:11.0pt;
font-family:"Aptos",sans-serif;}
span.spelle
{mso-style-name:spelle;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:11.0pt;
mso-ligatures:none;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:1088890155;
mso-list-template-ids:1523363886;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style>
</head>
<body lang="FR" link="#467886" vlink="#96607D" style="word-wrap:break-word">
<div class="WordSection1">
<div>
<p class="MsoNormal"><span lang="EN-US">Hello,<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">I haven’t seen this discussed anywhere yet. Our PhD student has been struggling to get her models judged by the PDB Validate server, as we usually do before submission to the PDB.<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">The problem seems to come when Validate tries to calculate the map and CCs. Upon discussion with the PDB crew, the instruction she had was to REMOVE lines 16-27 from the
<span class="spelle">mmcif</span> file. Then it worked. The contents of the unwanted lines are the following:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>loop_</i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>_entity.id</i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>_<span class="spelle">entity.type</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>A <span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>MG! non-<span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>ADP! non-<span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>VO4! non-<span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>ZZZ! non-polymer</i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>EDO! non-<span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>SO4! non-<span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i>CL! non-<span class="spelle">polymer</span></i></p>
<p class="MsoNormal" style="margin-left:70.8pt"><i><span lang="EN-US">water <span class="spelle">
water</span></span></i><span lang="EN-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">(I can’t publicly share the entire <span class="spelle">
mmcif</span> file at this point. “ZZZ” is a ligand )<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">Previous structures from her contained those lines and where accepted, so we believe there was a recent update in Validate that started to bother with them.<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">So for the next rounds of Validate, we’ll remove those lines before uploading – which is all right, but I just wanted:<o:p></o:p></span></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US">To warn you about this;<o:p></o:p></span></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1"><span lang="EN-US">To ask if you have other suggestions of routines, other than uploading to Validate for this kind of pre-submission test? We use the validation tools in Coot and
<span class="spelle">Molprobity</span>, but for some reason the criteria and the calculated maps are not exactly the same as for the PDB… It would be much easier to have this validation running locally, just to avoid the uploading interface.<o:p></o:p></span></li></ol>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> Looking forward to your replies,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">---------------------------------------------------<br>
Carlos KIKUTI, PhD<br>
UMR144 - CNRS - Institut Curie</span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Pavillon Trouillet Rossignol <br>
26 Rue d’Ulm - 75005 Paris, France<br>
+33 6 82 87 62 76<br>
</span><a href="mailto:carlos.kikuti@curie.fr" title="mailto:carlos.kikuti@curie.fr"><span style="font-family:"Calibri",sans-serif;color:#0563C1">carlos.kikuti@curie.fr</span></a></p>
</div>
</div>
<p class="MsoNormal"> </p>
</div>
</div>
</body>
</html>