/usr/share/pymol/examples/devel/cgo07.py is in pymol-data 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | from pymol.cgo import *
from pymol import cmd
from random import random, seed
from chempy import cpv
# CGO ellipsoids
# first draw some walls
obj = [
COLOR, 1.0, 1.0, 1.0,
BEGIN, TRIANGLE_STRIP,
NORMAL, 0.0, 0.0, 1.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 10.0, 0.0, 0.0,
VERTEX, 0.0, 10.0, 0.0,
VERTEX, 10.0, 10.0, 0.0,
END,
BEGIN, TRIANGLE_STRIP,
NORMAL, 1.0, 0.0, 0.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 0.0, 10.0, 0.0,
VERTEX, 0.0, 0.0, 10.0,
VERTEX, 0.0, 10.0, 10.0,
END,
BEGIN, TRIANGLE_STRIP,
NORMAL, 0.0, 1.0, 0.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 0.0, 0.0, 10.0,
VERTEX, 10.0, 0.0, 0.0,
VERTEX, 10.0, 0.0, 10.0,
END
]
seed(0x1)
def random_ellipsoid(box, size, min_axis):
# return a random ellipsoid record of the form:
# [ ELLIPSOID, x_pos, y_pos, z_pos, size, x0, y0, z0, x1, y1, z2, x2, y2, z2 ]
# where the xyz vectors are orthogonal and of length 1.0 or less.
box = box - size
tmp0 = cpv.random_vector()
tmp1 = cpv.random_vector()
tmp2 = cpv.cross_product(tmp1, tmp0)
tmp3 = cpv.cross_product(tmp1, tmp2)
tmp4 = cpv.cross_product(tmp2, tmp3)
tmp2 = cpv.normalize(tmp2)
tmp3 = cpv.normalize(tmp3)
tmp4 = cpv.normalize(tmp4)
primary = cpv.scale(tmp2, random())
secondary = cpv.scale(tmp3,random())
tertiary = cpv.scale(tmp4,random())
factor = 1.0 / max( cpv.length(primary), cpv.length(secondary), cpv.length(tertiary))
primary = cpv.scale(primary, factor)
secodary = cpv.scale(secondary, factor)
tertiary = cpv.scale(tertiary, factor)
return [ ELLIPSOID,
size + random() * box, size + random() * box, size + random() * box,
max(random() * size, min_axis),
] + primary + secondary + tertiary
for count in range(100):
# obj.extend( [ALPHA, random() ] )
obj.extend( [COLOR, random(), random(), random()] )
obj.extend( random_ellipsoid(10.0, 1.5, 0.2) )
# use more triangles when drawing ellipsoids
cmd.set('cgo_ellipsoid_quality', 2)
# then we load it into PyMOL
cmd.load_cgo(obj,'cgo07')
# rotate the view
cmd.turn('y',-45)
cmd.turn('x',30)
# zoom out a bit
cmd.zoom('all', 2)
# move the read clipping plane back a bit to brighten things up
cmd.clip('far',-5)
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