[modeller_usage] symmetry in automodel

[Gordon Wells <>]

Hi all

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.


-- 

"FABRICATI DIEM, PVNC"

	-- Terry Pratchett, Guards! Guards!

Gordon Wells
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria