<div dir="ltr">Marie<div><br></div><div>The validation of ligands performed by the PDB uses Mogul. If you have Mogul installed (free to most academic institutions, AFAIK), you can ask eLBOW to define the bonds and angles using Mogul thus providing geometry closer to the target. Discussions of whether this is a sound idea aside, you can avoid many of the validation issues. Metals are always tricky so for AD9 you may still be liaising with your annotator. I can send you a set of Mogul restraints for AD9 if desired. </div><div><br></div><div>Phenix and CCP4 ship with their own restraints libraries. You can point Phenix to the CCP4 libraries but you will remove some features from the Phenix tools. Either way, you can load a restraints dictionary that you have generated into Coot to do RSR etc.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif">Cheers</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Nigel</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">---</font></div><div><font face="arial, sans-serif">Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</font></div><div><font face="arial, sans-serif">Lawrence Berkeley National Laboratory</font><br><font face="arial, sans-serif">Berkeley, CA 94720-8235</font><br><font face="arial, sans-serif">Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></font></div></div><div><font face="arial, sans-serif"><span style="color:rgb(73,74,76)">ORCID : </span><font color="#494a4c"><a href="https://orcid.org/0000-0001-8857-9464" target="_blank">orcid.org/0000-0001-8857-9464</a></font></font><br></div></div></div></div></div></div></div><br></div><img src="https://pxl-mailtracker.com/pixel/ybIBjrYJDuPs9EmQJQoy?rid=ybIBjrYJDuPs9EmQJQoy" width="1" height="1" border="0"></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jun 10, 2021 at 6:12 AM Marie Elizabeth Fraser <<a href="mailto:frasm@ucalgary.ca">frasm@ucalgary.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello,<br>
<br>
The parameters we use as restraints for small molecules in complex with macromolecules have improved greatly, but we still get complaints when submitting to the Protein Data Bank. We use grade to obtain restraints for these small molecules, but when we submit to the PDB, some of their restraints do not match. I am not clear where the PDB gets these restraints, but we edit our file to match the values sent and finish the refinement. What do others do?<br>
<br>
As well, PHENIX and COOT aren’t accessing the same library for restraints. Is this due to how I’ve installed ccp4 (for COOT) and PHENIX?<br>
<br>
The small molecule whose restraints I currently need is ADP metavanadate (AD9), which grade won’t accept because of the vanadium, so I used elbow to calculate restraints.<br>
<br>
Thank you, Marie<br>
<br>
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