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 PE¥A 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

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