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Hello Pooja--
>
> Is it possible in XPLOR to calculate the orientation angle between
> the center of mass of the secondary structures or a specified segment?
>
I'm not 100% sure of what you're trying to calculate. You can simply
calculate centers of mass of secondary structure elements (or any
AtomSel). If these points define an angle, it too can be calculated:
from vec3 import Vec3, dot
cm=Vec3(0,0,0)
mass=0.
for atom in AtomSel("(name C or name CA or name N) and resid 40:50"):
cm += atom.mass() * atom.pos()
mass += atom.mass()
pass
cm /= mass
an angle:
from math import acos
theta=acos( dot(cm2-cm1,cm3-cm1) )
However, you need to somehow provide secondary structure definitions
> Is there anyway to constrain this angle to ensure the correct geometry ?
>
secondary structure elements can be contrained relative to each other
by grouping them together in a rigid body using the IVM. The following
in an IVM setup fixing residues 40-50 and 73-89 relative to each
other. All other atoms would undergo torsion angle dynamics.
from ivm import IVM
dyn = IVM()
dyn.group( "resid 40:50 or resid 73:89" )
protocol.torsionTopology(dyn)
hope this helps--
Charles
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