Hello,
I'm fairly new to modeller, and I'm trying to run a parallel job. I can't seem to get the 'from modeller.parallel import *' line to work. When I input it, no models are created. I have python 3.8 installed, and I'm not sure why it's happening. My script is below.
from modeller import *
from modeller.automodel import *
from modeller.parallel import *
j= job()
j.append(local_slave())
j.append(local_slave())
j.append(local_slave())
log.verbose()
env = environ()
env.io.atom_files_directory = ['.', './template_struc']
# create a subclass of automodel or loopmodel, MyModel.
# user can further modify the MyModel class, to override certain routine.
class MyModel(automodel):
def customised_function(self): pass
#code overrides the special_restraints method
#def special_restraints(self, aln):
#code overrides the special_patches method.
# e.g. to include the addtional disulfides.
#def special_patches(self, aln):
a = MyModel(env, sequence = tarSeq,
# alignment file with template codes and target sequence
alnfile = 'alignment.ali',
# PDB codes of the templates
knowns = template)
# index of the first model
a.starting_model = 1
# index of the last model
a.ending_model = 100
loopRefinement = False
# Assesses the quality of models using
# the DOPE (Discrete Optimized Protein Energy) method (Shen & Sali 2006)
# and the GA341 method (Melo et al 2002, John & Sali 2003)
a.assess_methods = (assess.GA341, assess.normalized_dope)
a.use_parallel_job(j)
a.make()
I'm still figuring my way out around this. Any help appreciated. Thanks.