Hej,

if you simply copy-paste the wiki entry into PyMOL you will get the error. This code is intended to be run as a block (e.g. from script) and creates e.g. problems with indentation, or other errors.
A simple solution would be to wrap the commands to a block using "python" and "python end".

Either you include them in what copy paste (the whole shabang):

python
# axes.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 (requires pymol version 0.8 or greater, I
# believe
 
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
 
# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
python end

OR you can enter the lines/ copy paste sequentially.

If you are interested in arrows/ cones, have a look at the cgo_arrow script:
http://www.pymolwiki.org/index.php/Cgo_arrow

Hope this helps.

Cheers,

Andreas


On Mon, Aug 25, 2014 at 5:48 PM, vincent Chaptal <vincent.chaptal@ibcp.fr> wrote:
Hi,

I'm trying to draw arrows in Pymol 1.7.2 for mac, "à la http://www.pymolwiki.org/index.php/Axes "

When I run the script for the Axes_with_nice_cones, I have the error message:
File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py", line 464, in parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1
    CONE, 0.0, 0.0,   l, 0.0, 0.0, h+l, d, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, 1.0]
                                                                                      ^
SyntaxError: invalid syntax


As a workaround, I tried to use the cylinder syntax (bellow, by replacing CYLINDER by CONE), pymol loads the object but doesn't draw anything.
cmd.load_cgo( [ CONE, x0, y0, z0, x1, y1, z1, radius, r1, g1, b1, r1, g1, b1 ], "cone_a" )


Can someone tell me what is going on and how I can draw a cgo CONE in pymol? It looks very nice.

Thank you
Vincent




--

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Protéines

Drug-resistance modulation and mechanism Laboratory

7 passage du Vercors 

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.ibcp.fr



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