no need to implement common linear algebra functions, there is the
chempy.cpv module shipped with pymol (and there is numpy as well).
Ramiro, I recently did something similar, just adjust the residue
selection in the code below (requires numpy):
python
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])
dir1 = plane_normal('A/37/CG+CD1+CE1+CZ+CE2+CD2')
dir2 = plane_normal('A/41/CG+CD1+CE1+CZ+CE2+CD2')
print 'Angle in degrees:', math.degrees(cpv.get_angle(dir1, dir2))
python end
Cheers,
Thomas
On Thu, 2010-09-23 at 13:02 +0200, Tsjerk Wassenaar wrote:
> Hi Ramiro,
>
> A bit of linear algebra wouldn't hurt... :p
> In python:
>
> def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
>
> def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
>
> def svmul(s,a): return s*a[0], s*a[1], s*a[2]
>
> def normalize(a): return svmul(1/math.sqrt(dot(a,a)),a)
>
> def cross(a,b): return a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2],
> a[0]*b[1]-a[1]*b[0]
>
> a = cmd.get_model('r. phe and i. ##RESIDUE1## and n. cg,ce1,ce2').atom
> a = [ i.coord for i in a ]
> b = cmd.get_model('r. phe and i. ##RESIDUE2## and n. cg,ce1,ce2').atom
> b = [ i.coord for i in b ]
>
> na = normalize(cross(vsub(a[1],a[0]),vsub(a[2],a[0])))
> nb = normalize(cross(vsub(b[1],b[0]),vsub(b[2],b[0])))
> angle = math.acos(dot(na,nb))
>
> print angle
>
> ###
>
> Haven't tested it, and there may be more efficient ways of getting the
> coordinates. If you run into problems like this more often, it's
> likely that you should pick up on algebra and programming... :)
>
> Have fun,
>
> Tsjerk
>
>
> On Thu, Sep 23, 2010 at 12:19 PM, Ramiro Téllez Sanz
> <urcind...@gmail.com> wrote:
> > Thanks for your kind help, Tsjerk.
> >
> >> Hi Ramiro,
> >>
> >> Assuming your rings are nicely planar, and representing the ring as:
> >>
> >> 1-2-3
> >> | |
> >> 6-5-4
> >>
> >> you can get the plane normal vector as the vector cross product from
> >> (3)-(1) and (5)-(1).
> >
> > OK. But I just started to use pymol. Which are the commands to do so?
> > I know how to get the coordinates of a selected atom, but need the pymol
> > commands to treat the data:
> > a) How to create the vectors from 1->3 and from 1->5
> > b) How to treat the vectors to perform the vector cross product
> >
> >> Doing so for both rings gives you the two normal vectors. The angle
> >> then follows from the dot product of the (normalized) normal vectors:
> >>
> >> angle = acos(n1 . n2)
> >
> > Again, I would need the commands to:
> > c) Normalize the vectors (how to set their modules = 1)
> >
> > I also guess n1 and n2 represent the normalized vectors, don't they? So
> > this command is very clear :)
> >
> >> It becomes a bit more elaborate if the planes are not planar :)
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >
> > Again, thanks very much in advance for your kind help.
> >
> >> On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz
> >> <urcind...@gmail.com> wrote:
> >>>
> >>> Hi everyone and thanks for reading this!
> >>>
> >>> I am interested in measuring the angle between aromatic ring planes.
> >>> Is there any easy way/script to do it?
> >>>
> >>> One way that came to my mind is creating a pseudoatom representing the
> >>> centroid for each ring (I already know how to do that), then drawing two
> >>> lines perpendicularly to the planes from both centroids, and finally
> >>> measuring the angle between the lines. Will that be possible? How could
> >>> this be done?
> >>>
> >>> Is there any other way? I'm completely clueless. Any help will be
> >>> greatly appreciated.
> >>>
> >>> Thanks in advance,
> >>>
> >>> Ramiro Tellez Sanz
> >>> Dept. Physical Chemistry
> >>> University of Almeria
> >>> Spain
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology /
> University of Groningen
> The Netherlands
--
Thomas Holder
Group of Steffen Schmidt
Department of Biochemistry
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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