<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:10pt;color:#000000;font-family:Verdana,Geneva,sans-serif;" dir="ltr">
<p style="margin-top:0;margin-bottom:0">Dear all,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="margin-bottom: 0in">I am trying to refine a complete virus pdb structure (possessing icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not supported". So, I followed
a previous post in phenixbb: <a href="http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html" id="LPlnk272827" previewremoved="true">
http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html</a> and merged multiple models into one but faced following problems:
</p>
<p style="margin-bottom: 0in"><br>
</p>
<p style="margin-bottom: 0in">1. This merged file is unreadable in UCSF Chimera.</p>
<p style="margin-bottom: 0in">2. The secondary structure definition in the PDB file header is not recognizable anymore in Phenix.</p>
<p style="margin-bottom: 0in"><br>
</p>
<p style="margin-bottom: 0in">In my understanding, both the problems are arising due to PDB format's inability to handle more than 62 chains and 99999 atoms in a file. So, what will be the work-around to perform a real space refinement of the complete virus
structure at once? Also, how to maintain secondary structure during such refinement? </p>
<p style="margin-bottom: 0in"><br>
</p>
<p style="margin-bottom: 0in">Any help is highly appreciated.</p>
<br>
<p></p>
<p style="margin-top:0;margin-bottom:0">Best regards,</p>
<p style="margin-top:0;margin-bottom:0">Tofayel</p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 10pt; color: rgb(117, 123, 128); font-family: Verdana, Geneva, sans-serif;"><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="color: rgb(117, 123, 128); font-family: Verdana, Geneva, sans-serif; font-size: 10pt;">............................................</span><br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; background-color:rgb(255,255,255)">
<p style="color:rgb(0,0,0)"><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:12pt"></span></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:12pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p style="color:rgb(0,0,0)"><span style="color:rgb(117,123,128); font-size:10pt; font-family:Verdana,Geneva,sans-serif">Tofayel Ahmed</span></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:12pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p><font color="#757b80"><span style="font-size:10pt; font-family:Verdana,Geneva,sans-serif">Graduate Student (PhD) | Lab-</span><span style="font-size:10pt; font-family:Verdana,Geneva,sans-serif">02n-01</span></font></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p><font color="#757b80"><span style="font-size:10pt; font-family:Verdana,Geneva,sans-serif">School of Biological Sciences</span></font></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:12pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p><span style="color:rgb(117,123,128); font-size:10pt; font-family:Verdana,Geneva,sans-serif">Nanyang Technological University</span><br>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:12pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p style="color:rgb(0,0,0)"><span style="font-size:12pt; color:rgb(117,123,128)"><span style="color:rgb(117,123,128); font-family:Verdana,Geneva,sans-serif; font-size:10pt">60 Nanyang Drive, Singapore 637551</span><br>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span></span></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p style="color:rgb(0,0,0)"><span style="color:rgb(117,123,128)"></span><span style="font-size:12pt; color:rgb(117,123,128)"><span style="font-size:10pt; font-family:Verdana,Geneva,sans-serif">+65 8650.0473 |</span></span><a href="mailto:tahmed.pcu@gmail.com" target="_blank" style="color:rgb(17,85,204); font-family:verdana,sans-serif; font-size:small" id="LPNoLP"><span style="font-size:10pt; font-family:Verdana,Geneva,sans-serif">tofayel001@e.ntu.edu.sg</span></a></p>
<p></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:12pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span>
<p class="MsoNormal" style="color:rgb(0,0,0)"></p>
<span style="font-family:Verdana,Geneva,sans-serif; font-size:10pt"></span><span style="font-family:Georgia,serif; font-size:12pt"></span><span style="font-size:10pt; font-family:Verdana,Geneva,sans-serif"> </span><br>
<p style="color:rgb(0,0,0)"></p>
<p style="color:rgb(0,0,0)"></p>
<p style="color:rgb(0,0,0)"><span style="font-size:12pt"></span></p>
</div>
</div>
</div>
</body>
</html>