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from pymol import cmd
from chempy.models import Indexed
from chempy import Atom,Bond
import math
# create a model instance
model = Indexed()
# append the atoms onto it
for x in range(-63,63,1):
for y in range(-63,63,1):
new_atom = Atom()
new_atom.symbol = 'O'
new_atom.coord = [ x*2, y*2, 30 * math.cos(math.sqrt(x*x+y*y)/60.0) ]
model.atom.append(new_atom)
cmd.load_model(model,"membrane")
cmd.hide("everything","membrane")
cmd.show("spheres","membrane")
cmd.color("lightblue","membrane")
cmd.set_view( (\
0.736728907, -0.144400939, 0.660589039,\
0.675238073, 0.208899528, -0.707400322,\
-0.035847016, 0.967217624, 0.251406968,\
0.000008686, 0.000009686, -332.961212158,\
-2.366872311, -1.122793436, 23.127344131,\
11.627288818, 654.294433594, 0.000000000 ))
# uncomment this if you programmable shaders
# cmd.set("sphere_mode",5)
# uncomment if you have lotsa RAM
# cmd.set("hash_max",240)
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