Re: [modeller_usage] Side chain dihedral angles

[Modeller Caretaker <>]

On 4/1/10 6:01 AM, abdullah ahmed wrote:
> I wanted to asked if there is a way to restrain the side-chain dihedrals
> to angles of my choosing. If so could you please provide a brief sample
> code of how to do it?

Yes, of course - you can add a custom dihedral restraint, e.g. to 
harmonically restrain chi1 in a CYS residue to 90 degrees, you could use:

a = mdl.atoms
dih = features.dihedral(a['N:1'], a['CA:1'], a['CB:1'], a['SG:1'])
mdl.restraints.add(forms.gaussian(group=physical.chi1_dihedral,
                                  feature=dih,
                                  mean=math.pi/2.,
                                  stdev=0.01))

You might also want to look at forms.cosine which is commonly used for 
restraining dihedrals.

	Ben Webb, Modeller Caretaker
--
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