<div dir="ltr">Alisia<div><br></div><div>It seems your request relies on the perception that restraints are not allowed to exceed a certain point. It is much more complicated than a hard limit as it's an optimisation that involves the EM data, the ideal restraints values, the ESD values of said restraints and even the starting geometry of the ligand. Have you validated the final geometry with something like Mogul?</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></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Dec 6, 2021 at 2:01 AM Fadini, Alisia <<a href="mailto:alisia.fadini15@imperial.ac.uk">alisia.fadini15@imperial.ac.uk</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">
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Hello, </div>
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I am trying to use phenix.real_space_refine to improve the fit between my protein's ligand and the electron density. </div>
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I include a CIF file that has worked well for reciprocal space refinement, made through JLigand.</div>
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It seems to me that the CIF file is read properly, it does not produce errors and the restrains are stated correctly in the output .cif file that includes all protein + ligand atoms. However, the output pdb shows a distorted ligand, where specific bond angles
and bond lengths have been modified past what should be allowed by the restrains. </div>
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Any insights on how to improve/the causes of this effect would be very welcome! </div>
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My command is : <span style="font-size:10pt"><i>phenix.real_space_refine model.pdb map.ccp4 ligand.cif resolution=1.63</i></span></div>
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<span style="font-size:12pt"><i></i>Thank you,</span><span style="font-size:10pt"><i><br>
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<span style="font-size:12pt">Alisia</span></div>
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