axes_cyl.py

from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
   CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
   CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
   CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,

   ]

# add labels to axes object

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3.0,0.0,0.0],[0.0,3.0,0.0],[0.0,0.0,3.0]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')