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.pyfrom pymol.cgo import *from pymol import cmdfrom 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 PyMOLcmd.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>
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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