<html xmlns:v="urn:schemas-microsoft-com:vml" 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=us-ascii">
<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;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Times New Roman",serif;
color:windowtext;
font-weight:normal;
font-style:normal;
text-decoration:none none;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-NZ" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">I have a case where we have crystallised a ligand in our protein and the ligand purchased is a mixture of 4 structural isomers (enantiomers and diastereomers). There is no way of telling
if one over the other is bound in the active site so we have assumed all 4 are binding. I have generated 4 separate ligands with 4 separate cifs and the all fit the density. I am refining the complex with all 4 ligands at 0.25 occupancy (occupancy refinement
is switched off, I have changed the clash guard non-bonded distance threshold is set to 0.0 (as an initial error message came up with nonbonded interactions < 0.5).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">My refinement ran to completion, but something is definitely not right. The pdb file won’t load in Coot and in pymol the ligands have imploded/exploded. I am just wondering if this is the
best way to refine this structure (or I have missed something) and probably more to the point what have I missed with the ligands. To me it is almost identical to alternate conformations, but I have obviously missed something<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">I have just install phenix 1.10 on a windows machine.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif">J<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:EN-NZ">_________________________________</span><span style="color:black;mso-fareast-language:EN-NZ"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:EN-NZ">Joel Tyndall, PhD<br>
<br>
Associate Professor in Medicinal Chemistry<br>
National School of Pharmacy<br>
University of Otago<br>
PO Box 56 Dunedin 9054<br>
New Zealand </span><span style="color:black;mso-fareast-language:EN-NZ"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:EN-NZ">Skype: jtyndall<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:EN-NZ"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:EN-NZ">Ph: +64 3 479 7293<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>