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Hello 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 ? a.make() 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
log.verbose()
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
a.make()
Attachment:
Loop_refine.log
Description: Loop_refine.log