Hi,
Try to use this command to call DOPE score: assess_methods=(assess.DOPE, assess.GA341))
a = MyModel(env, alnfile = 'Template-Model.ali', knowns = ('TEMPLATE'), sequence = 'MODEL', assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1 # index of the first model
a.ending_model = 1000 # index of the last model (determines how many models to calculate)
a.make() # do the actual homology modeling
Then, select the best 5 models with lowest DOPE score:
# 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])
Regards,
Flavio
-------------------------------------
Flavio Augusto Vicente
Seixas
Laboratory of Structural Biochemistry
Department of Biochemistry
Universidade Estadual de Maringá, PR, Brazil
http://www.uem.br
From: Modeller Caretaker <modeller-care@salilab.org>
To: HERBERT MAX VENTHUR PEĽA <h.venthur01@ufromail.cl>; modeller_usage@salilab.org
Sent: Tuesday, December 17, 2013 1:19 AM
Subject: Re: [modeller_usage] DOPE for multiple template-based homology modeling