Re: [modeller_usage] parallel modeling _automodel class

[Modeller Caretaker <>]

On 7/13/16 11:37 AM, Sajad Ahrari wrote:
> I am trying to do a parallel job for protein loop refinement by
> MODELLER9.17. I prepared the scripts as follows and provided all the
> input files in my working directory and I am running MODELLER through
> python2.7 (by typing: "python ModellerModelling.py" ). Although I
> encounter no error through the modeling process, but I doubt if I am
> doing a parallel job since when I check my workstation CPU usage, only
> one CPU is engaged (the usage percent does not exceed 100%). Could you
> please help me know what am I missing?

There are many errors in your scripts, but the most fundamental problem 
is that the customized "MyModel" class should only be declared, not 
instantiated, in mymodel.py. All of the logic should be in the file you 
run (ModellerModeling.py). So you want something like

ModellerModeling.py:

from modeller import *
from modeller.automodel import *
from modeller.parallel import *
from mymodel import MyModel

j = job()
for i in range(16):
    j.append(local_slave())

env = environ()
a = MyModel(env, alnfile=..., etc.)
a.starting_model=...
a.ending_model  =...
a.use_parallel_job(j)
a.make()



mymodel.py:

from modeller import *
from modeller.automodel import *

class MyModel(loopmodel):
    def select_loop_atoms(self):
        from modeller import selection
        return selection(
            self.residue_range('256', '309'))
    def select_atoms(self):
        from modeller import selection
        return selection(
            self.residue_range('256', '309'))

	Ben Webb, Modeller Caretaker
--
             https://salilab.org/modeller/
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