[modeller_usage] Unpick restraints and partial optimization.

[Gregoire Depret <>]

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.

-- 
Depret Grégoire
Graduate Student


Service de Structure et Fonction des Membranes Biologiques
Centre de Biologie Structurale et de Bioinformatique
Université Libre de Bruxelles
Boulevard du Triomphe CP 206/2
B-1050 Bruxelles
Belgium