<div dir="ltr">Hi, Pavle<div><br></div><div>When I use phenix.hbond to generate hbond.eff, it reports an error as the cif file for the ligand is missing.</div><div>When I use the following commands, it says cif file is not used.</div><div>phenix.hbond model.pdb ligand.cif</div><div>or</div><div>phenix.hbond model.pdb files=ligand.cif</div><div><br></div><div>What will be the right syntax to include cif for phenix.hbond?</div><div><br></div><div>Thanks!</div><div><br></div><div>Charles</div><div><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Oct 20, 2022 at 7:26 PM Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</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">Hi Charles,<br>
<br>
it should be as simple as<br>
<br>
phenix.geometry_minimization model.pdb ligand.cif<br>
<br>
However, note that geometry restraints used in this case are very <br>
simplistic, for example, there are no attraction term. This means <br>
helices may unfold unless you do a good thorough job defining secondary <br>
structure restraints (and generally restrain all known hydrogen bonds). <br>
You can do this by making a hydrogen bond restraint file:<br>
<br>
phenix.hbond model.pdb<br>
<br>
(model.pdb needs to have explicit H added)<br>
<br>
and then supply that file to the above minimization command:<br>
<br>
phenix.geometry_minimization model.pdb ligand.cif hbond.eff<br>
<br>
It may be a good idea to verify hbond.eff to make sure it is as complete <br>
and accurate as possible. This is because H-bond definitions in this <br>
file are made based on input model and if input model geometry isn't <br>
great, the H-bond annotations (and corresponding restraints) may not be <br>
accurate either.<br>
<br>
In summary, here are the steps:<br>
<br>
1) Add H to the model:<br>
<br>
phenix.ready_set model.pdb<br>
<br>
2) Make H-bond restraints definitions:<br>
<br>
phenix.hbond model_with_H.pdb<br>
<br>
This command will create hbonds_pymol.pml file that you can load into <br>
PyMol and see all H bonds as dashed line. This lets you verify all H <br>
bonds that the program found (or missed). Edit hbond.eff if needed.<br>
<br>
3) Finally, run geometry regularization:<br>
<br>
phenix.geometry_minimization model.pdb ligand.cif hbond.eff<br>
<br>
Let me know if you have any questions! Good luck,<br>
<br>
Pavel<br>
<br>
On 10/19/22 19:04, CPMAS Chen wrote:<br>
> Hi, All,<br>
><br>
> I have a structure calculated with NMR restraints but it has quite <br>
> some geometry violation, such as torsion angles, clashes etc.<br>
> The structure has a small molecule ligand bound.<br>
><br>
> Is it possible to add an CIF file for the ligand and use <br>
> phenix.geometry_minimization to idealize/optimize the protein structure?<br>
><br>
> I have tried the following and phenix reported an error for missing <br>
> CIF file.<br>
><br>
> phenix.geometry_minimization model.pdb <br>
> pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif<br>
><br>
> what would be the correct syntax to add ligand cif for this <br>
> geometry_minimization?<br>
><br>
> Or what would be the proper way to idealize/optimize a protein <br>
> structure with ligands present?<br>
><br>
> The structure optimization during NMR calculation is not good enough <br>
> in my case.<br>
><br>
> Thanks!<br>
><br>
> Charles<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>
<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Instructor</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p><p></p></div></div></div>