Dear Modeller users, I am trying to unselect some restraints of the restraint file coming from my homology model in order to perform some optimization. Following the recommandations, I have tried the unpick method like this.
mdl = complete_pdb(env, 'homo_model.pdb') mdl.restraints.append(file='./original_restraints.rsr') mdl.rename_segments(segment_ids=('A', 'A', 'B'), renumber_residues=(32, 98, 693)) allrest = selection(mdl) mdl.restraints.pick(allrest) mdl.restraints.unpick(mdl.residue_range('706:B', '736:B')) mdl.restraints.condense()
I get the following logfile
runcmd______> restraints.append(file='./original_restraints.rsr') runcmd______> model.rename_segments(segment_ids=('A', 'A', 'B'), renumber_residues=(32, 98, 693)) runcmd______> restraints.pick((def)residue_span_range=(0, 99999), (def)restraint_sel_atoms=1, (def)restraints_filter={'default':-999 .000000}) runcmd______> restraints.unpick() unpick__441_> Number of restraints unselected: 0 condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 101301 101301
None of the restraints were removed. Since I renumber my model I have tried the restraint.reindex command but I didn't make it through either. I know I can edit my restraint file and remove the unwanted restraints but I can't find my residues back in the homology generated restraint file, I only read atom index.
Another question. I want to perform an optimization on some parts of my model only. I have tried to add residue ranges to a selection and then optimize this selection, but in this case modeller don't take into account the unselected parts of my model and I get overlapping helices. I understand why It is happpening nevertheless is there still a way to achieve partial optimization without overlapping ? Many thanks for your answers.