Hi Richard,
* Richard Gillilan <[email protected]> [2007-02-19 10:22] wrote:
>
> I'm probably making a simpler mistake here, or perhaps there is
> something wrong with my installation or paths.
> I'm trying to load and display the simple cgo example in the manual.
> I created a file named "arrows" containing this definition:
>
> from pymol.cgo import * # get constants
> from pymol import cmd
>
> obj = [
> BEGIN, LINES,
> COLOR, 1.0, 1.0, 1.0,
>
> VERTEX, 0.0, 0.0, 0.0,
> VERTEX, 1.0, 0.0, 0.0,
>
> VERTEX, 0.0, 0.0, 0.0,
> VERTEX, 0.0, 2.0, 0.0,
>
> VERTEX, 0.0, 0.0, 0.0,
> VERTEX, 00, 0.0, 3.0,
>
> END
> ]
>
> From the Pymol prompt I then attempt to load it:
>
> PyMOL> cmd.load_cgo(obj,'/Volumes/transport/AFABP_structs/Linoleic4/
> rf10_TLS/arrows');
>
> I get the following error:
>
> Traceback (most recent call last):
> File "/Users/delwarl/MacPyMOL060228/build/Deployment/MacPyMOL.app/
> pymol/modules/pymol/parser.py", line 370, in parse
> File "<string>", line 1, in ?
> NameError: name 'obj' is not defined
>
> Anyone recognize what I am doing wrong here?
The cmd.load_cgo command wants the object and object name as parameters,
so you want to put the load_cgo command within your file and use the run
command to load it (it is a python file):
# --------- arrows.py ---------------------------
from pymol.cgo import * # get constants
from pymol import cmd
obj = [
BEGIN, LINES,
COLOR, 1.0, 1.0, 1.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 1.0, 0.0, 0.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 0.0, 2.0, 0.0,
VERTEX, 0.0, 0.0, 0.0,
VERTEX, 00, 0.0, 3.0,
END
]
cmd.load_cgo(obj,'arrows')
Load it into PyMOL with:
PyMOL> run arrows.py
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<[email protected]> http://adelie.biochem.queensu.ca/~rlc
