[Date Prev ][Date Next ][Thread Prev ][Thread Next ][Date Index ][Thread Index ]
Re: [modeller_usage] Excluded volume/Planar spatial restraint
To : Shyam Saladi <saladiATcaltech.edu >, modeller_usageATsalilab.org
Subject : Re: [modeller_usage] Excluded volume/Planar spatial restraint
From : Modeller Caretaker <modeller-careATsalilab.org >
Date : Wed, 22 Feb 2017 17:52:09 -0800
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
--
modeller-careATsalilab.org https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage