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Re: [modeller_usage] DOPE for multiple template-based homology modeling



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 <>
To: HERBERT MAX VENTHUR PE¥A <>;
Sent: Tuesday, December 17, 2013 1:19 AM
Subject: Re: [modeller_usage] DOPE for multiple template-based homology modeling

On 12/16/13 6:46 AM, HERBERT MAX VENTHUR PE¥A wrote:
> Recently, I performed homology modeling using multiple templates with
> success (following the advanced tutorial). However, I could not pick a
> specific structure because I didn't find a dope score into the log file.
> Is there any posibility to obtain this dope score for multiple
> templates-based models?.

DOPE is an assessment score. It doesn't care anything about how you
generated the models, so calculating it for multiple template modeling
and single template modeling is identical.

    Ben Webb, Modeller Caretaker
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