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/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
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Researcher, Carnegie Mellon University, Computational Biology Department