Hi, Pavle When I use phenix.hbond to generate hbond.eff, it reports an error as the cif file for the ligand is missing. When I use the following commands, it says cif file is not used. phenix.hbond model.pdb ligand.cif or phenix.hbond model.pdb files=ligand.cif What will be the right syntax to include cif for phenix.hbond? Thanks! Charles On Thu, Oct 20, 2022 at 7:26 PM Pavel Afonine wrote:

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 ******************************************************