[modeller_usage] Unpick restraints and partial optimization.

[Gregoire Depret <gdepret AT ulb.ac.be>]

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

gdepret AT ulb.ac.be
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