Hi Madhu,
1. Is there a way of applying antibumping restraints to decrease the number of clashes in phenix.refine, I looked at older posts but couldn't get a satisfactory guideline regarding the same.
The antibumping restraints (nonbonded interactions) are on by default. Currently there isn't a syntax to turn them off or to change the default parameterization. If you refine for a few cycles with the weight for the x-ray target set to zero (wxc_scale=0) the clashes should definitely go away. Then go back to normal refinement (wxc_scale=0.5). I'd hope that the clashes don't come back. Otherwise that's what the x-ray data guide the minimization to, even though the restraints are pushing back.
2. The default setttings for geometry refinement looks like this: refinement.geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } Do I have to change "dihedrals=True"
This will not work: Sorry: Invalid atom selection: refinement.geometry_restraints.remove.dihedrals="True" (RuntimeError: Syntax error.) You have to specify atom selections to *remove* default restraints.
if I do not want to put restraints on dihedrals. I was thinking that one puts restraints on psi/phi angles only by setting "discard_psi_phi = False" because when I set it to "discard_psi_phi = True", the Ramachandran plot was much better. But I did not want to do this because then the Ramachandran plot is no more a validation tool. I just wanted to know if Unknowingly I did that by setting up "dihedrals = None".
No, if you leave the geometry_restraints.remove block untouched you'll get all restraints incl. dihedrals, except for the peptide psi and phi angles, which are controlled by the dedicated parameter you quote. Cheers, Ralf