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[modeller_usage] (no subject)


I have been doing the tutorial http://salilab.org/modeller/wiki/Missing%20residues

I have generated the alignment.ali file containing the pdb file 1qg8 and the 1qg8_fill sequences. (I basically copied them from the web site). I have gotten “automodel” to work without any problems. However, when I try run “loopmodel” it fails. Again, I am using the script directly from the web site for loop modeling (attached). When I attempt to run it, Modeller loads it libraries etc but then fails with the following error printed, not in log, but to the screen.


 File “loop-refine.py”, line 19, in ?



Does anyone have any insights as to what I could be doing incorrect?


Thanks, Steve

from modeller import *
from modeller.automodel import *    # Load the automodel class

env = environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

a = loopmodel(env, alnfile = 'alignment.ali',
              knowns = '1qg8', sequence = '1qg8_fill')
a.starting_model= 1
a.ending_model  = 1

a.loop.starting_model = 1
a.loop.ending_model   = 2
a.loop.md_level       = refine.fast


Attachment: Loop_refine.log
Description: Loop_refine.log