[modeller_usage] error in using a simulated structure as template.

[Bala subramanian <bala.biophysics@gmail.com>]

Friends,
I am a newbie to modeller. I have the structure of a protein obtained from MD simulation (total 339 residues). I have another sequences of unknown structure ( total 345 residues). I want to model the structure of the later by using the simulated structure as template. 

I first aligned the two sequences with clustwal  and made the .ali file (pasted below) . The modeller script i used is attached. Kindly write me what is going wrong ?

The following is the ali file.

 >P1; temp
 structureM:temp:1 :A:339 :A ::::
 VVLENVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVGAGSCDTSVITQACPK
 ISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAE
 EEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNQNTRKSIHI--GPGRAFYTTGEIIGDI
 RQAHCNISRAKWNDTLKQIVIKLREQF-ENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCN
 SAQLFNSTWNN---NTEGSNNTEG-NTITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCS
 SNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIE*
 >P1; targ
 sequence:targ::::::::
 VVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPK
 VSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAE
 EEVVIRSANFTDNAKTIIVQLNQSVEINCTRPNNNTRKSIRIQRGPGRAFVTIGK-IGNM
 RQAHCNISRAKWNATLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCN
 STQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQFINMWQEVGKAMYAPPISGQIRCS
 SNITGLLLTRDGGNNNNGSEIFRPGGGDMRDNWRSELYKYKVVKIE*

I get the following error when i run the command mod9v8 model.py

'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "model.py", line 11, in ?
    a.make()
  File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 98, in make
    self.homcsr(exit_stage)
  File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 424, in homcsr
    self.check_alignment(aln)
  File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 406, in check_alignment
    aln.check()
  File "/apps/modeller/9v8//modlib/modeller/alignment.py", line 200, in check
    self.check_structure_structure(io=io)
  File "/apps/modeller/9v8//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 :

Thanks,
Bala


#!/usr/bin/env python	
from modeller import *
from modeller.automodel import *

log.verbose()
env = environ()
env.io.atom_files_directory = ['.','../atom_files']
a = automodel(env, alnfile = 'temp-tar.ali', knowns = 'temp', sequence = 'targ')
a.starting_model= 1
a.ending_model = 1
a.make()