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Hi,
I generated 100 models of a protein and now I would like to select the 20 with the lowest DOPE score. I tried to use the script provided in the manual but it gave an error (see below).
To generate the models (models were obtained sucessfully):
# Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys
log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
# Read in HETATM records from template PDBs env.io.hetatm = True
a = AutoModel(env, alnfile='ahr-mult.ali', knowns=('3f1o_pasA','3h7w_pasA','3h82_pasA'), sequence='AhR', assess_methods=(assess.DOPE))
a.starting_model= 1 # index of the first model a.ending_model = 100 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling
To sort the models by DOPE score:
# Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys
log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in
# Get a list of all successfully built models from a.output ok_models = [x for x in a.outputs if x['failure'] is None
# Rank the models by DOPE score key = 'DOPE score' if sys.version_info[:2] == (2,3): ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key])
# Get top model m = ok_models[0] print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key])) Error shown:
File "model-output.py", line 17 key = 'DOPE score' ^ SyntaxError: invalid syntax I also tried to combine the scripts as shown in the manual (same error):
# Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys
log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
# Read in HETATM records from template PDBs env.io.hetatm = True
a = AutoModel(env, alnfile='ahr-mult.ali', knowns=('3f1o_pasA','3h7w_pasA','3h82_pasA'), sequence='AhR', assess_methods=(assess.DOPE))
a.starting_model= 1 # index of the first model a.ending_model = 100 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling
# Get a list of all succesfully built models from a.output ok_models = [x for x in a.outputs if x['failure'] is None
# Rank the models by DOPE score key = 'DOPE score' if sys.version_info[:2] == (2,3): ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key])
# Get top model m = ok_models[0] print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key]))
Error shown:
File "model-output.py", line 27 key = 'DOPE score' ^ SyntaxError: invalid syntax
Best,
Amanda F. Ghilardi |