<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:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Dear all, Dear Pavel,</p>
<p><br>
</p>
<p>I have encountered a problem where a new bond was generated between the O of SO4 and O(H) of my ligand (with a glycerol head group, I call it glycerol here).
<br>
</p>
<p><br>
</p>
<p>As shown in the figure in the Dropbox link below, I have placed the glycerol (purple) in the density and it fits well. The distance between the O of SO4 and the OH of glycerol was 2.55 angstrom. After refinement (yellow) however, the glycerol was pulled
out of density with the distance changed to 1.27 angstrom, therefore forming a new bond.
<br>
</p>
<p><br>
</p>
<p>When hydrogens were added to the glycerol, the glycerol was again pulled, forming a C-O bond between SO4 and glycerol.
<br>
</p>
<p><br>
</p>
<p>When the positions (xyz) of the glycerol atoms were fixed, the SO4 was pulled towards glycerol, making a O-O bond between SO4 and glycerol.
<br>
</p>
<p><br>
</p>
<p><span>When the positions of the SO4 and glycerol were both fixed during the refinement, the result came out saying the bond length was too long between the the O (SO4) and the O (glycerol).
<br>
</span></p>
<p><span><br>
</span></p>
<p><span><span>Thus I thought Phenix must treated it as a covalent bond. </span></span><br>
</p>
<p><br>
</p>
<p>I have tried Rafmac and it did not do this to the model. The cif files etc were the same for Phenix and Rafmac.</p>
<p><br>
</p>
<p>The problem appeared both on version 1.10-2152 and the latest version 1.10.2155.</p>
<p><br>
</p>
<p>How could I fix this problem?</p>
<p><br>
</p>
<p>Many thanks,</p>
<p><br>
</p>
<p>Jingyi Hu<br>
</p>
<p><br>
</p>
<p><a id="LPlnk918456" href="https://www.dropbox.com/s/3i53kvlmds591f5/phenix-SO4-new-bond.png?dl=0" class="OWAAutoLink">https://www.dropbox.com/s/3i53kvlmds591f5/phenix-SO4-new-bond.png?dl=0</a></p>
<div style="margin-bottom: 20px; overflow: auto; width: 100%; text-indent: 0px;" id="LPBorder_GT_14697079946490.14137559435150193">
<table style="width: 90%; background-color: rgb(255, 255, 255); position: relative; overflow: auto; padding-top: 20px; padding-bottom: 20px; margin-top: 20px; border-top: 1px dotted rgb(200, 200, 200); border-bottom: 1px dotted rgb(200, 200, 200);" id="LPContainer_14697079946220.4582779171342579" cellspacing="0">
<tbody>
<tr style="border-spacing: 0px;" valign="top">
<td colspan="2" style="vertical-align: top; position: relative; padding: 0px; display: table-cell;" id="TextCell_14697079946430.5852126623856327">
<div id="LPRemovePreviewContainer_14697079946430.17879956654156637"></div>
<div style="top: 0px; color: rgb(0, 120, 215); font-weight: 400; font-size: 21px; font-family: "wf_segoe-ui_light","Segoe UI Light","Segoe WP Light","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; line-height: 21px;" id="LPTitle_14697079946430.12144968112199983">
<a target="_blank" href="https://www.dropbox.com/s/3i53kvlmds591f5/phenix-SO4-new-bond.png?dl=0" style="text-decoration: none;" id="LPUrlAnchor_14697079946450.7348069301877359">phenix-SO4-new-bond.png</a></div>
<div style="margin: 10px 0px 16px; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; font-size: 14px; line-height: 14px;" id="LPMetadata_14697079946460.8908489486648506">
www.dropbox.com</div>
<div style="display: block; color: rgb(102, 102, 102); font-weight: 400; font-family: "wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; font-size: 14px; line-height: 20px; max-height: 100px; overflow: hidden;" id="LPDescription_14697079946470.03940681483342334">
Shared with Dropbox</div>
</td>
</tr>
</tbody>
</table>
</div>
<br>
<p></p>
</div>
</body>
</html>