[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] symmetry in automodel

Gordon Wells wrote:
Is it possible to impose symmetry restraints in automodel? I've tried the following: 

def defsym(mdl, aln, seg1, seg2):
    for (set,seg) in [(2,seg1), (3,seg2)]:
        mdl.pick_atoms(aln, pick_atoms_set=set,selection_segment=seg,
                       atom_types='ALL',selection_status='INITIALIZE',
                       selection_search='SEGMENT')
    mdl.symmetry.define(symmetry_weight=1.0,add_symmetry=(True,False))

segsize = 330
class symmodel(automodel):
    def special_restraints(self, aln):
        defsym(self,aln,seg1=('1',str(segsize)), 	
	seg2=(str(segsize+1),str(2*segsize)))
	defsym(self,aln,seg1=(str(segsize+1),str(2*segsize)),
	seg2=(str(2*segsize+1),str(3*segsize)))

The commands are accepted, but have no effect on the final model.
That looks fine to me - you should definitely be able to impose symmetry restraints in automodel.
One thing to watch out for (which I can't check, because you didn't include the whole script): make sure you create a 'symmodel' object, not an 'automodel' one, otherwise you won't get your customized restraints. See http://salilab.org/modeller/manual/node31.html 

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage