Hi Ramiro,
> * How do I adjust the code with my selected rings? Do I need to include
> both residues in the same selection in pymol, then rename the selection,
> and then include the chosen selection name in the code where you write
> "selection"?
you need two selections of two residues, in my example the part 'A/37/CG
+CD1+CE1+CZ+CE2+CD2' is the selection on chain A, residue 37 and ring
atoms.
> * How do I run the code after I adjust it with my "selection"? I have
> never run a python program from within pymol. What should I do?
I put the code (including Tsjerk's additions!) to a file, see attached.
You have to run it with pymol (File > Run...) and then call the
ring_angle command.
Example to get angle between aromatic residues 37 and 41 in chain A:
ring_angle chain A and resi 37, chain A and resi 41
Cheers,
Thomas
from pymol import cmd, stored
from chempy import cpv
import numpy, math
def plane_normal(selection):
stored.x = list()
cmd.iterate_state(-1, selection, 'stored.x.append([x,y,z])')
x = numpy.array(stored.x)
U,s,Vh = numpy.linalg.svd(x - x.mean(0))
return cpv.normalize(Vh[2])
def ring_angle(selection1, selection2, quiet=1):
a = plane_normal(selection1 + " and not (e. h or n. c,n,ca,cb,o,oxt)")
b = plane_normal(selection2 + " and not (e. h or n. c,n,ca,cb,o,oxt)")
deg = math.degrees(cpv.get_angle(a, b))
if not int(quiet):
print 'Angle in degrees: %.2f' % (deg)
return deg
cmd.extend("ring_angle",ring_angle)
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