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]
------------------------------------- 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.