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