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

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Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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