Dear Modeller

This is python file which i am giving to run multichain modeling :

# Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class

log.verbose()

# Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0)

env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']

# Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'twochain.ali' , # alignment filename knowns = '3RHW', # codes of the templates sequence = 'hGLR') # code of the 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 model-multichain.py lines 1-37/37 (END)

But i get following error:

Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-multichain.py", line 37, in ? a.make() # do homology modeling File "/usr/lib/modeller9.9/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib/modeller9.9/modlib/modeller/automodel/automodel.py", line 424, in homcsr self.check_alignment(aln) File "/usr/lib/modeller9.9/modlib/modeller/automodel/automodel.py", line 406, in check_alignment aln.check() File "/usr/lib/modeller9.9/modlib/modeller/alignment.py", line 200, in check self.check_structure_structure(io=io) File "/usr/lib/modeller9.9/modlib/modeller/alignment.py", line 209, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :

May i kindly know how can i solve this problem....