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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Xinghua:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">A couple of questions you might ask before reverting to drastic measures:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Can you exclude a covalent bond to the protein?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">How confident are you about the fit, orientation and nature of the ligand?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Do you see the same phenomenon in a different dataset, i.e. is it reproducible?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It is better to look for an explanation of your experimental findings than to tweak/restrain the refinement to conform to your expectations.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">At this resolution the occupancy will be tightly coupled to B-factors. You could try and refine an overall occupancy for the ligand. What makes you believe
that you have partial occupancy? Residual fofc density? <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Carsten<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<b>On Behalf Of </b>xinghuaqin@126.com<br>
<b>Sent:</b> Monday, August 10, 2015 10:43 PM<br>
<b>To:</b> phenixbb<br>
<b>Subject:</b> [phenixbb] ligand refinement<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">Hi everyone,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">I am refining a structure of protein/ligand complex (2.75 </span><span style="font-size:11.5pt;color:black;background:white">Å</span><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black;background:white">)
almost to the last stage. However, I found that some atoms of the ligand is too close to the protein (1.2 or 1.3 </span><span style="font-size:11.0pt;color:black;background:white">Å</span><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black;background:white">)
after refinement.</span><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">How should I avoid this? Should I use the "nonbonded_distance_cutoff" parameter? What the value should be set to?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">Another question is that at this resolution is it possible for me to refine the occupancy?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">Any suggestion is appreciated.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black"><br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">Best<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black">Xinghua<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Microsoft YaHei","sans-serif";color:black"><o:p> </o:p></span></p>
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<p style="line-height:17.85pt"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black;background:white">Xinghua Qin Ph.D</span><span style="font-size:10.5pt;font-family:"Arial","sans-serif";color:black"><o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black">Department of Physiology<br>
The Fourth Military Medical University<br>
169# Changlexi Road<br>
Xi'an 710032, China<br>
Tel. 86-29-84772779</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p></o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black">E-mail: <a href="mailto:xinghuaqin@126.com" target="_blank"><em><span style="font-family:"Verdana","sans-serif";color:black">xinghuaqin@126.com</span></em></a></span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p></o:p></span></p>
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