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
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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
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 >
On 11/29/2011 03:03 AM, flavio seixas wrote: > 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.
Just build a new comparative model using the regular automodel class, using your original model as the template. Use a simple alignment containing two copies of the model sequence. Override select_atoms() as per the example at http://salilab.org/modeller/9.10/manual/node23.html to define the region to refine.
Note, however, that Modeller models generally do not need refinement (and if they do, using Modeller to do it probably won't make the models any better!)
> 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.
Loop refinement can be used for any region without a template. The protein can adopt any secondary structure, including an alpha helix. But yes, typically loop refinement will give you coil structures.
Ben Webb, Modeller Caretaker
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flavio seixas -
Modeller Caretaker