Hi PyMOL users,

thank you for your help. I tried to apply Carsten's suggestions using the LINE_STRIP approach. This is what I tested:

from pymol.cgo import *    # get constants
from pymol import cmd

obj = [
LINEWIDTH, 50,
BEGIN, LINE_STRIP,
COLOR, 255, 0, 0,
VERTEX, 11.335700035095215, 7.798659801483154, 7.798659801483154,
VERTEX, 11.335700035095215, 5.352089881896973, 5.352089881896973,
VERTEX, 14.965800285339355, 5.352089881896973, 5.352089881896973,
VERTEX, 14.965800285339355, 7.798659801483154, 7.798659801483154,
VERTEX, 11.335700035095215, 7.798659801483154, 7.798659801483154,
END
   ]                                                                                           

cmd.load_cgo(obj,'cgo01')

where four atoms make up a square. This snippet creates - when called by "run <path-to-script>" - four lines between these coordinates I got by using "print cmd.get_model('<selection-name>', 1).get_coord_list()". How can I have the the area between those four points filled with a colour of my choice and have it be partly transparent? The next step would be to create polyhedra with corresponding surfaces with atoms spanning a three dimensional object.

Thanks in advance
Timo