Before launching phenix.varref, I would like to generate a
ligand restraint file so the ligand doesn't fly away from its
density.
It would be great if the ligand_restraints.eff file could be
generated from a PDB file already containing the ligand (for
example originating from refinement), that we can then edit
afterwards. The ligand I'm talking about is ATP in this case, so
it doesn't need external cif file for refinement.
I searched but couldn't identify such a job. It would be useful
if it could be added to "PDB tools" or similar.