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?
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()