Hi Vincent,

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.

you need to define what in Phenix is called custom bond restraints: some "dummy" bonds between pairs of ligand and protein atoms of your choice. These bonds will anchor the ligand in place. Let me know if you need help setting up those but I think I sent you an example some time ago.
While generating such a file automatically is possible it may not be fool-proof as it will depend on the geometric quality of the model. So it's best to use your chemical intuition to choose those pairs of atoms that you'd like to link.

Good luck!
Pavel