Dear All,

I am using modeller for the first time. Before mentioning the problems I am facing, please allow me to mention my goals to be performed by modeller.

I already have a BLAST generated fasta alignment file. I need to convert the fasta alignment to PIR format, and generate the comparative model.

May I please request you to let me know how this goal can be achieved.

Moreover, after installing the modeller tarball package for ubuntu x86_64, when running the script to convert the fasta alignment to PIR I get this error.

/media/deepak/modeller/bin/ python
Traceback (most recent call last):
  File "", line 2, in <module>
    from modeller import *
  File "/media/deepak/Nourhan/deepak_research2016/NM_005343_NM_002880_RAS_RAF/", line 3, in <module>
    env = environ()
NameError: name 'environ' is not defined
import sys, os
from modeller import *
env = environ()
a = alignment(env, file='NM_005343-native-protein.fasta', alignment_format='FASTA')
a.write(file='NM_005343-native-protein.pir', alignment_format='PIR')

Thank you so much for your time and consideration.



Researcher, Carnegie Mellon University,
Computational Biology Department