Re: [modeller_usage] How to select rigid restraints with certain residues ?
To: Mahesh Velusamy <>,
Subject: Re: [modeller_usage] How to select rigid restraints with certain residues ?
From: Modeller Caretaker <>
Date: Thu, 23 Jun 2016 16:57:31 -0700
On 6/23/16 8:55 AM, Mahesh Velusamy wrote:
Actually, I try to do optimization on set of selected atoms with random
deviation 100 .
Why do you want to do that? That'll basically destroy your input
structure - you may as well not have one at all.
Then later I realized that I cant keep random deviation
more than 0.5 for following these residue (HIS,TRY,TYR,PHE)
Right, randomize_xyz() won't randomize ring structures too much, as what
tends to happen in this case is that the optimizer can't recover the
correct structures afterwards.
s=selection(mdl1.atoms['CA:'+respos+':'+chain].select_sphere(10))#selected
set for optimization
r = rigid_body(selection(s).only_residue_types('HIS,TYR,TRP,PHE'))# By
this I select atoms of HIS,PHE from selected set to keep rigid
mdl.restraints.rigid_bodies.append(r)
But, This doesn't work
Doesn't work how? randomize_xyz() should work fine with rigid bodies -
it just won't do any rotation:
selection.only_residue_types() takes a space-separated list of residue
types, not comma-separated. So most likely you're trying to build a
rigid body containing zero atoms.
I'm not quite sure what you want to do, but if you want to randomly move
a set of atoms as a rigid body, just select them all and then use
selection.transform() or the various selection translate and rotate methods: