Re: [modeller_usage] Excluded volume/Planar spatial restraint

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 2/22/17 2:28 PM, Shyam Saladi wrote:
> I would like to specify some sort of planar spatial
> restraint to describe where the residues can be, e.g. residues allowed
> above 10 A in the z direction? Is there a way to specify this?

Sure, that's straightforward. See 
https://salilab.org/modeller/9.18/manual/node28.html for adding 
additional restraints to the modeling and 
https://salilab.org/modeller/9.18/manual/node108.html for the restraints 
themselves. You probably want something like a harmonic lower bound on 
the z coordinate, e.g.

rsr.add(forms.lower_bound(group=physical.xy_distance,
                          feature=features.z_coordinate(at['CA:35']),
                          mean=10.0, stdev=0.1))

(This would restrain the CA atom in residue 35.)

	Ben Webb, Modeller Caretaker
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