Dear Modeller users,

I would like to model only a segment of my protein, precisely res 76 - 94. I am using model-segment.py script for this purpose. I have looked at the existing example on web (http://salilab.org/modeller/9v1/manual/node22.html). I created alignment file with the same protein. I have no problems running the script but the model obtained is exactly the same as the template which is expected but even the residue range 76-94 is exactly the same.

I am pasting my script here, please let me know where am I going wrong? ------------------------------------------------------------------------------ from modeller import * from modeller.automodel import * # Load the automodel class

log.verbose()

class MyModel(automodel): def select_atoms(self): # Select residues 1 and 2 (PDB numbering) return selection(self.residue_range('76:', '94:'))

env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # selected atoms do not feel the neighborhood env.edat.nonbonded_sel_atoms = 2

# Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = '5tmg-5tmg.ali', # alignment filename knowns = '5tmgA', # codes of the templates sequence = '5tmg') # code of the target

a.starting_model= 1 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling

------------------------------------------------------------------------------

Many Thanks, Lipi