[modeller_usage] Loop Model ranking

[flavio seixas <>]

Hi Ben

First of all I would like to apologise for a so basic question. However, I am not a pyton expert and do not have another one to ask here.

I run the loop.py scritp to generate 200 models.

However, my attempt to rank the models by DOPE score fails.

I am using the script below:

############################################
from modeller import *
from modeller.automodel import *

log.verbose()
env = environ()

env.io.atom_files_directory = ['.', '../atom_files']

# Read in HETATM records from template PDBs
env.io.hetatm = True

# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms
class MyLoop(loopmodel):
    # This routine picks the residues to be refined by loop modeling
    def select_loop_atoms(self):
        # Two residue ranges (both will be refined simultaneously)
        return selection(self.residue_range('23:A', '25:A'),
                         self.residue_range('73:A', '75:A'))

m = MyLoop(env, inimodel='Modeloutput23.pdb', sequence='Target1', loop_assess_methods=(assess.DOPE, assess.GA341))

m.loop.starting_model= 1           # index of the first loop model
m.loop.ending_model  = 200         # index of the last loop model
m.loop.md_level = refine.very_fast  # loop refinement method

m.make()

# Get a list of all successfully built models from a.outputs
ok_models = filter(lambda x: x['failure'] is None, a.outputs)

# Rank the models by DOPE score
key = 'DOPE score'
ok_models.sort(lambda a,b: cmp(a[key], b[key]))

# Get top model
m = ok_models[0]

print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[1]

print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[2]

print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[3]

print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[4]

print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key])

##############################

I realise that "loop assess methods" could not be the same sintax for "model assess methods", but I do not know how to correct it in the script

Could you give me any help?

Thanks in advance,

Flavio