Hi Wulf,
I would like to unrestrain the distance between two atoms in a ligand – how can I do this? I found instructions for writing a remove_restraints_selections.params file in the phenix.refine manual, but it does not seem to address bond distances.
bonds are not there indeed. Currently you can do it as following (admittedly rather ugly!)... Edit ligand CIF file to remove the definition of bond in question, then run refinement providing this CIF file. If CIF file is part of Phenix library, then a) Find its location: elbow.where_is_that_cif_file ATP you will see something like this /Users/pafonine/phenix_dev/modules/chem_data/mon_lib/a/ATP.cif b) Copy it to your place cp /Users/pafonine/phenix_dev/modules/chem_data/mon_lib/a/ATP.cif ATP_edited.cif Then edit ATP_edited.cif to remove the bond in question (I guess you would want to remove angle too) and give it to phenix.refine along with all other inputs. Let me know how this worked (or didn't) for you! Pavel