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Re: [modeller_usage] Add rigid bodies and CA-CA restraints

Gregoire Depret wrote:

To avoid that kind of kinks I want to treat the helices as rigid bodies.
First I tried to add rigid bodies in the same script

a = mymodel(env,
            alnfile  = 'align.pir',     # alignment filename
            knowns   = '2OXS',     # codes of the templates
            sequence = 'mytemplate ')       # code of the target

r = rigid_body(a.residue_range('180:B', '200:B'))
s = rigid_body(a.residue_range('890:C', '900:C'))
a.restraints.rigid_bodies.append(r)
a.restraints.rigid_bodies.append(s)
But in this case, MODELLER doesn't recognize the residue range, and raises the error "No such Residues 180:B". I have checked in previous models; the residues are there.
You can't make restraints before you call a.make(), because the model coordinates don't exist at that point. To add any restraints (including rigid bodies), define the special_restraints routine: http://salilab.org/modeller/manual/node26.html 

	Ben Webb, Modeller Caretaker
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