<div dir="ltr">Vincent<div><br></div><div>Can you send me your model?</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">Email : NWMoriarty@LBL.gov</font></div><div><font face="arial, sans-serif">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 Fri, Sep 15, 2023 at 7:46 AM vincent Chaptal <<a href="mailto:vincent.chaptal@ibcp.fr">vincent.chaptal@ibcp.fr</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">
<div>
<font size="4"><font face="monospace">Hi Pavel, <br>
<br>
yes I do have the file which goes : <br>
<br>
</font></font>geometry_restraints {<br>
edits {<br>
bond {<br>
atom_selection_1 = chain A and resseq 1601 and name O2<br>
atom_selection_2 = chain A and resseq 895 and name OG<br>
distance_ideal = 3.2 <br>
sigma = 0.5<br>
}<br>
bond {<br>
atom_selection_1 = chain A and resseq 1601 and name O2<br>
atom_selection_2 = chain A and resseq 299 and name OG<br>
distance_ideal = 2.3 <br>
sigma = 0.5<br>
}<br>
<br>
.... many more bonds.... <br>
<br>
}<br>
}<br>
<br>
But it takes some time to generate a good amount of restraints, and
for structures with several ligands it could be a long task. <br>
Agreed that it is not fool-proof but a general edition of these
bonds and editing afterwards would be a good little program I
believe. <br>
<br>
Best<br>
Vincent<br>
<br>
<br>
<div>Le 15/09/2023 à 14:34, Pavel Afonine a
écrit :<br>
</div>
<blockquote type="cite">
<p>Hi Vincent,<br>
</p>
<blockquote type="cite"><font size="4"><font face="monospace"> Before launching
phenix.varref, I would like to generate a ligand restraint
file so the ligand doesn't fly away from its density. <br>
It would be great if the ligand_restraints.eff file could be
generated from a PDB file already containing the ligand (for
example originating from refinement), that we can then edit
afterwards. The ligand I'm talking about is ATP in this
case, so it doesn't need external cif file for refinement.<br>
<br>
I searched but couldn't identify such a job. It would be
useful if it could be added to "PDB tools" or similar. </font></font><br>
</blockquote>
<p><br>
you need to define what in Phenix is called custom bond
restraints: some "dummy" bonds between pairs of ligand and
protein atoms of your choice. These bonds will anchor the ligand
in place. Let me know if you need help setting up those but I
think I sent you an example some time ago.<br>
While generating such a file automatically is possible it may
not be fool-proof as it will depend on the geometric quality of
the model. So it's best to use your chemical intuition to choose
those pairs of atoms that you'd like to link.<br>
</p>
<p>Good luck!<br>
Pavel</p>
<p><br>
</p>
<br>
</blockquote>
<br>
<div>-- <br>
<p><span>Vincent Chaptal, PhD</span></p>
<p><span>Director of GdR APPICOM</span></p>
<p><span>Drug Resistance and Membrane
Proteins Lab</span></p>
<p><span></span><br>
</p>
<p><span>MMSB -UMR5086</span></p>
<p><span>7 passage du Vercors<span> </span></span></p>
<p><span>69007 LYON</span></p>
<p><span>FRANCE</span></p>
<p><span>+33 4 37 65 29 01</span></p>
<p><span><a href="http://www.appicom.cnrs.fr" target="_blank">http://www.appicom.cnrs.fr</a></span></p>
<p><span><a href="http://mmsb.cnrs.fr/en/" target="_blank">http://mmsb.cnrs.fr/en/</a></span></p>
<p><span><br>
</span></p>
</div>
</div>
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