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<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We have been finalising a structure with a ligand complexed to heme. I have been checking the close to final structure and I noticed that the ligand looks distorted away from what one would expect. We use Phenix.refine<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">We initially used the grade server for our restraints files. I also just used elbow to generate a new one. Looking at both, the restraints look reasonable (similar in both) however the initial output pdb from elbow is distorted further.
The angles /lengths looked reasonable and are similar to small molecule structures (CCDC).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The planarity of a bi-phenyl moiety is very distorted.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><img width="573" height="326" style="width:5.9687in;height:3.3958in" id="Picture_x0020_1" src="cid:image001.png@01D72248.0AB91390"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Are we missing something?<o:p></o:p></p>
<p class="MsoNormal">Do we need to tell phenix.refine to not over refine the model?<o:p></o:p></p>
<p class="MsoNormal">Should elbow give a distorted model?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Apologies if this is all online but my uni cant seem to access phenix.org!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Joel<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;color:#365F91;mso-fareast-language:EN-NZ">Joel Tyndall |</span><span lang="EN-US" style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;color:#0070C0;mso-fareast-language:EN-NZ">
</span><span style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;color:#555555;mso-fareast-language:EN-NZ">BSc(Hons) PhD</span><span lang="EN-US" style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;mso-fareast-language:EN-NZ"><br>
<span style="color:#0070C0"><br>
</span><span style="color:#365F91">Associate Professor in Medicinal Chemistry<br>
School of Pharmacy |</span><span style="color:#0070C0"> </span><span style="color:#595959">He Rau Kawakawa</span><span style="color:#0070C0"><br>
</span><span style="color:#365F91">University of Otago |</span><span style="color:#0070C0">
</span></span><span style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;color:#555555;mso-fareast-language:EN-NZ">Te Whare W</span><span style="font-size:9.0pt;color:#555555;mso-fareast-language:EN-NZ">�</span><span style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;color:#555555;mso-fareast-language:EN-NZ">nanga
o Ot</span><span style="font-size:9.0pt;color:#555555;mso-fareast-language:EN-NZ">�</span><span style="font-size:9.0pt;font-family:"Gill Sans MT",sans-serif;color:#555555;mso-fareast-language:EN-NZ">go<o:p></o:p></span></p>
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Skype: jtyndall<o:p></o:p></span></p>
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