Hi Amit (and other users),
Here's a script which can be used to put marks on the positions of every
atom in a selection. There are several types of marks included now, e.g.
cube, rhombic dodecahedron, tetrahedron, plus and star. Using a matrix
operator these can be extended a bit, to 2D counterparts for example, or
to elongated or rotated shapes. I should still include some
documentation but in brief the usage is as follows:
graph selection = '(all)', shape = 'plus' | 'sphere' | 'star' |
'tetrahedron' | 'dodecahedron', size = 1, r = 0.10, rgb1 = [1,0,0], rgb2
= [0,0,1], mtx = [[1,0,0],[0,1,0],[0,0,1]], name = "graph"
Selection should be obvious, as is shape. Size is a relative indicator
for the size, though at present I haven't fixed things such that a size
1 tetrahedron matches a size 1 dodecahedron. r is the radius of the
lines. rgb1 and rgb2 are the start and end color for each line. mtx is
the matrix operator, which works on the original shape centered around
the origin (before translation to the point of the atom from the selection).
Hope this already works a bit as wanted. I'll be trying to make it a bit
better in the future ;)
Cheers,
Tsjerk
Amit Chourasia wrote:
Tsjerk,
Great I'll look forward to see your script.
By that time I'll also gain some familiarity with Python.
For spline related stuff I found this in archive.
set ribbon_trace,1
This will create ribbons for arbitrary atoms, but they should be seperate
objects if we dont want them connected by one ribbon.
Have a nice time in Rome. I wish to travel to Venice sometime.
Thanks and Regards
--Amit
-----Original Message-----
From: Tsjerk Wassenaar [mailto:t.a.wassen...@chem.rug.nl]
Sent: Thursday, May 13, 2004 3:04 AM
To: a...@sdsc.edu
Subject: Re: [PyMOL] 3d plotting in pymol
Hi Amit,
This isn't too difficult actually, and I have done something alike
recently. What it comes down to is to write some python extensions and
have definitions for the CGO shapes you want to use. Then you can read
the coordinates for the atoms ( sel =
cmd.get_selection("selection_string") and reading coordinates from
sel.atom[i].coord ) and add these coordinates to your CGO object. Doing
this for all atoms and loading it back into pymol would give you what
you want. I'm not completely sure where I have the script I wrote. But I
can have a look in about a week (when I get back from Rome) and write
the script if it hasn't been done already (the feature sounds cool
enough ;) ).
Wouldn't have ideas on the spline at this moment.
Cheers,
Tsjerk
Amit Chourasia wrote:
Hi,
I am trying to use pymol as a 3d plotting tool.
I have few questions
1)Is there a way to add represenation in pymol. ?
For instance I would like to see the atom as a triangle or nhedron.
I was going through CGO objects that looks promising to what I want to
accomplish. What I am looking for is to add represenation module and
use them.
2)Is there a method to represent a group of atoms connected by cartoon
even if the chains are not biologically feasable. What I am looking
for is you have bunch of points(atoms) through which the ribbon should
pass like a spline curve.
Any inputs and pointers would be most appreciated.
Thanks
--Amit
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) Tsjerk A. Wassenaar, M.Sc.
-- :) Molecular Dynamics Group
-- :) Dept. of Biophysical Chemistry
-- :) University of Groningen
-- :) Nijenborgh 4
-- :) 9747 AG Groningen
-- :) The Netherlands
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-- :) Copy me into your ~/.signature to help me spread!
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) Tsjerk A. Wassenaar, M.Sc.
-- :) Molecular Dynamics Group
-- :) Dept. of Biophysical Chemistry
-- :) University of Groningen
-- :) Nijenborgh 4
-- :) 9747 AG Groningen
-- :) The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) Hi! I'm a .signature virus!
-- :) Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
from pymol.cgo import *
from pymol import cmd
from math import *
## Multiplying a vector b by matrix a ##
def mvmult(a, b):
return [ a[0][0]*b[0]+a[0][1]*b[1]+a[0][2]*b[2],
a[1][0]*b[0]+a[1][1]*b[1]+a[1][2]*b[2],
a[2][0]*b[0]+a[2][1]*b[1]+a[2][2]*b[2] ]
## Multiplying a vector b by scalar a ##
def svmult(a, b):
return [a*b[0], a*b[1], a*b[2]]
#-------- Definition of shapes
#
#PROTOTYPE:
#
# def shape(
# position=[0,0,0], Position
# size=1, General size
# axisradius=0.1, Axis radius for cylinders
and sausages
# rgb1=[1,1,1], Color, or start color for
cylinders and sausages
# rgb2=[1,1,1], End color for cylinders and
sausages
# mtx=[[1,0,0],[0,1,0],[0,0,1]]) Matrix operator for
deformation
#
def
sphere(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
obj = [SPHERE, position[0], position[1], position[2], 0.5*axisradius,
rgb1[0], rgb1[1], rgb1[2]]
return obj
def
plus(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
lines = [ [ [-0.5, 0.0, 0.0],[ 0.5, 0.0, 0.0] ],
[ [ 0.0,-0.5, 0.0],[ 0.0, 0.5, 0.0] ],
[ [ 0.0, 0.0,-0.5],[ 0.0, 0.0, 0.5] ] ]
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
def
star(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
cos60 = 0.5*sqrt(3)
sin60 = 0.5
lines = [ [ [-0.5, 0.0, 0.0],[ 0.5, 0.0, 0.0] ],
[ [-sin60, cos60, 0.0], [ sin60,-cos60, 0.0] ],
[ [-sin60,-cos60, 0.0], [ sin60, cos60, 0.0] ],
[ [-sin60, 0.0, cos60], [ sin60, 0.0,-cos60] ],
[ [-sin60, 0.0,-cos60], [ sin60, 0.0, cos60] ] ]
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
def
cube(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
lines = [ [ [-0.5,-0.5,-0.5], [ 0.5,-0.5,-0.5] ],
[ [-0.5,-0.5,-0.5], [-0.5, 0.5,-0.5] ],
[ [-0.5,-0.5,-0.5], [-0.5,-0.5, 0.5] ],
[ [ 0.5, 0.5, 0.5], [-0.5, 0.5, 0.5] ],
[ [ 0.5, 0.5, 0.5], [ 0.5,-0.5, 0.5] ],
[ [ 0.5, 0.5, 0.5], [ 0.5, 0.5,-0.5] ],
[ [-0.5, 0.5,-0.5], [ 0.5, 0.5,-0.5] ],
[ [-0.5, 0.5,-0.5], [-0.5, 0.5, 0.5] ],
[ [-0.5,-0.5, 0.5], [ 0.5,-0.5, 0.5] ],
[ [-0.5,-0.5, 0.5], [-0.5, 0.5, 0.5] ],
[ [ 0.5,-0.5,-0.5], [ 0.5, 0.5,-0.5] ],
[ [ 0.5,-0.5,-0.5], [ 0.5,-0.5, 0.5] ] ]
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
def
tetrahedron(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
a = [0,1,0]
cos104_90 = cos(pi*104.90/180)
sin104_90 = sin(pi*104.90/180)
sin120 = sin(pi*120/180)
cos120 = cos(pi*120/180)
b = mvmult([[cos104_90, sin104_90, 0],[-sin104_90,cos104_90,0],[0,0,1]],a)
c = mvmult([[cos120, 0, sin120],[0,1,0],[-sin120,0,cos120]],b)
d = mvmult([[cos120, 0, sin120],[0,1,0],[-sin120,0,cos120]],c)
lines = [ [ a, b ],
[ a, c ],
[ a, d ],
[ b, c ],
[ b, d ],
[ c, d ]]
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
def
tetrahedron1(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
a = [0,1,0]
cos104_90 = cos(pi*104.90/180)
sin104_90 = sin(pi*104.90/180)
sin120 = sin(pi*120/180)
cos120 = cos(pi*120/180)
b = mvmult([[cos104_90, sin104_90, 0],[-sin104_90,cos104_90,0],[0,0,1]],a)
c = mvmult([[cos120, 0, sin120],[0,1,0],[-sin120,0,cos120]],b)
d = mvmult([[cos120, 0, sin120],[0,1,0],[-sin120,0,cos120]],c)
lines = [ [ [0,0,0], a ],
[ [0,0,0], b ],
[ [0,0,0], c ],
[ [0,0,0], d ]]
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
def
rdodec(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
# vertices:
# The base cube, centered around (0,0,0)
a = [ 0.5, 0.5, 0.5 ]
b = [ 0.5, 0.5, -0.5 ]
c = [ 0.5, -0.5, 0.5 ]
d = [ 0.5, -0.5, -0.5 ]
e = [ -0.5, 0.5, 0.5 ]
f = [ -0.5, 0.5, -0.5 ]
g = [ -0.5, -0.5, 0.5 ]
h = [ -0.5, -0.5, -0.5 ]
# The conjugated octahedron of the base cube
i = [ 1.0, 0.0, 0.0 ]
j = [ 0.0, 1.0, 0.0 ]
k = [ 0.0, 0.0, 1.0 ]
l = [ -1.0, 0.0, 0.0 ]
m = [ 0.0, -1.0, 0.0 ]
n = [ 0.0, 0.0, -1.0 ]
lines = [ [ i, a ],
[ i, b ],
[ i, c ],
[ i, d ],
[ j, a ],
[ j, b ],
[ j, e ],
[ j, f ],
[ k, a ],
[ k, c ],
[ k, e ],
[ k, g ],
[ l, e ],
[ l, f ],
[ l, g ],
[ l, h ],
[ m, c ],
[ m, d ],
[ m, g ],
[ m, h ],
[ n, b ],
[ n, d ],
[ n, f ],
[ n, h ] ]
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
def
octahedron(position=[0,0,0],size=1,axisradius=1,rgb1=[1,1,1],rgb2=[1,1,1],mtx=[[1,0,0],[0,1,0],[0,0,1]]):
obj = []
for i in lines:
i[0] = mvmult(mtx,i[0])
i[1] = mvmult(mtx,i[1])
i[0] = svmult(size,i[0])
i[1] = svmult(size,i[1])
obj.extend([SAUSAGE,
i[0][0] + position[0], i[0][1] + position[1], i[0][2] +
position[2],
i[1][0] + position[0], i[1][1] + position[1], i[1][2] +
position[2],
axisradius, rgb1[0], rgb1[1], rgb1[2], rgb2[0], rgb2[1],
rgb2[2]])
return obj
shapefunctions = {"sphere": sphere,
"plus": plus,
"star": star,
"cube": cube,
"tetrahedron": tetrahedron,
"rdodec": rdodec,
"octahedron": octahedron}
def graph(sel="(all)", shape="plus", size=1, r=0.10, rgb1=[1,0,0],
rgb2=[0,0,1], mtx=[[1,0,0],[0,1,0],[0,0,1]], name="graph"):
sel = cmd.get_model(sel)
ln = len(sel.atom)
obj = []
for i in range(ln):
(x, y, z) = sel.atom[i].coord
obj.extend(shapefunctions[shape](sel.atom[i].coord,size,r,rgb1,rgb2,mtx))
cmd.load_cgo(obj, name)
cmd.extend('graph',graph)
