Re: [modeller_usage] How to select rigid restraints with certain residues ?

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

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:
https://salilab.org/modeller/9.16/manual/node251.html

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:
https://salilab.org/modeller/9.16/manual/node249.html

	Ben Webb, Modeller Caretaker
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