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