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/modpy.sh python modeller.py
Traceback (most recent call last):
File "modeller.py", line 2, in <module>
from modeller import *
File "/media/deepak/Nourhan/deepak_research2016/NM_005343_NM_002880_RAS_RAF/modeller.py", line 3, in <module>
env = environ()
NameError: name 'environ' is not defined
modeller.py:
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.
Sincerely,
Deepak
_____________
Researcher, Carnegie Mellon University,
Computational Biology Department