Hi there,
I have this py file to include disulfide bonds:
from modeller import * from modeller.automodel import *
class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['85:B'],self.residues['111:B'])) log.verbose() env = environ()
a = mymodel(env, alnfile = 'multiple.ali', knowns = ('1', '2'), sequence = '3', assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1 a.ending_model = 10
a.make()
# 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: %s (DOPE score %.3f)" % (m['name'], m[key])
I want to include hidrogens to the protein and a substrate that's on one of the templates to make a simulated annealing. And by the way, modeller does not make simmulated annealing wrigth?
Atila Iamarino wrote: > I have this py file to include disulfide bonds:
Looks good to me.
> I want to include hidrogens to the protein
That's straightforward - just subclass the allhmodel class rather than automodel, i.e. replace the line class mymodel(automodel): with class mymodel(allhmodel):
You should be aware that including hydrogens will result in your models taking roughly 4 times as long to build (since you have roughly twice as many atoms).
> and a substrate that's on one > of the templates
Just add relevant BLK residues ("." characters) to your alignment, and turn on env.io.hetatm. See the examples in the manual and tutorial.
> And by the way, > modeller does not make simmulated annealing wrigth?
I'm not sure what you mean. If you mean, "does Modeller do simulated annealing?" then yes, it does. The standard model building procedure combines conjugate gradients minimization with molecular dynamics simulated annealing refinement.
Ben Webb, Modeller Caretaker
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Atila Iamarino -
Modeller Caretaker