Hi Ben,
I was studing Modeller manual and I am not sure if there is a routine in modeller that can refine only part of an existin model, like loop refinement do. However, the region that I am interested to refine is not a loop. Because of this, I can not use loop refinement in helical segments, even though a region of three residues.
Is that right?
Regards,
Flavio
--- On Sat, 11/26/11, flavio seixas oivalf_nix@yahoo.com wrote:
> From: flavio seixas oivalf_nix@yahoo.com > Subject: [modeller_usage] Refine part of an existing model > To: "Modeller Usage" modeller_usage@salilab.org > Date: Saturday, November 26, 2011, 5:18 PM > Hi Modellers > > I generated a 1000 models of a protein using Modeller. > The best one shows 3 residues in disallowed regions of > Ramachandram plot. > I want to refine only regions around those 3 residues which > are in helical segments. > The script I am using in is not working. > Unfortunately I am not familiar with pyton script. > The error message and script file are as follow: > > > > > File "model-segment.py", line 35 > a = MyModel(env, inimodel='182.pdb', > sequence='Seq-target') > ^ > SyntaxError: invalid syntax > > --------------------------------------------------------------------------- > > from modeller import * > from modeller.automodel import * # Load the > automodel class > > log.verbose() > > env = environ() > > env.io.atom_files_directory = ['.', '../atom_files'] > > # selected atoms do not feel the neighborhood > env.edat.nonbonded_sel_atoms = 2 > > env.io.hetatm = True > > class MyModel(automodel): > def select_atoms(self): > # Select residues (PDB > numbering) > return > selection(self.residue_range('72:A', '75:A'), > > (self.residue_range('165:A', > '167:A'), > > (self.residue_range('199:A', > '201:A')) > > > # Be sure to use 'MyModel' rather than 'automodel' here! > a = MyModel(env, inimodel='182.pdb', > sequence='Seq-target') > > > a.starting_model= 1 > # index of the first model > a.ending_model = 1 > # index of the last model > > > # (determines how many models to > calculate) > a.make() > # do > homology modeling > > > > Could someone help me in this regard? > Thanks for any help. > > Flavio > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >