Dear All,
Actually, I try to do optimization on set of selected atoms with random deviation 100 . Then later I realized that I cant keep random deviation more than 0.5 for following these residue (HIS,TRY,TYR,PHE) and I have PHE and HIS in my selected set.
So , I decided to keep the atoms of HIS,PHE as rigid by following these commends:
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 So could you tell me how to select atoms of (HIS,TYR,TRP,PHE) residues from selection to make rigid ?
Thanking you in advance
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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Mahesh Velusamy -
Modeller Caretaker