Re: [modeller_usage] Refine part of an existing model

29 Nov 2011


      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
> 
> 
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