[modeller_usage] multichain modeling

[MUSTAFA BUGHIO <>]

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....


-- 
MUSTAFA BUGHIO

Junior Research Fellow
Lab # P-133
Computational Medicinal Chemistry and Drug Design
Panjwani Center For Molecular Medicine and Drug Research, International
Center for Chemical Sciences, University of Karachi, Karachi 75270
Pakistan, +923313425010