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 pymolimport 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.chap...@ibcp.fr <mailto:vincent.chap...@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 <tel:%2B33%204%2037%2065%2029%2001>
http://www.ibcp.fr
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