PyMOL Molecular Graphics System

Hmmm.

With a little messing around, it seems that this works at the pymol prompt:

for x in range(10): cmd.label("(name ca and resi %d)" % x, '"%s%s\" %
(resi, resn)')

The only difference is in the quoting. Double quotes inside single quotes.

gilleain

On 7/4/07, Clark, Louis <Louis.Clark@...> wrote:
>
>
>
>
> Dear user-group,
>
>   I'm trying to learn how to use python commands inside pymol .pml scripts.
> I seem to be missing some understanding about how the interface works.
> Could somebody tell me how to fix this command below?
>
>
>
> PyMOL>for x in range(10): cmd.label("(name ca and resi %d)" % x, "%s%s"
>
> PyMOL>% (resi, resn))
>
> Traceback (most recent call last):
>
>   File "/usr/local/pymol/modules/pymol/parser.py", line
> 232, in parse
>
>     exec(com2[nest]+"\n",pymol_names,pymol_names)
>
>   File "<string>", line 1, in ?
>
> NameError: name 'resi' is not defined
>
>
>
> thanks much!!
>
>
>
> -Louis
>
>
>
> Louis Clark, Ph.D.
>
> louis.clark@...
>
>
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>

Hi Louis,

* Clark, Louis <Louis.Clark@...> [2007-07-04 12:01] wrote:
> Dear user-group,
> 
>   I'm trying to learn how to use python commands inside pymol .pml
> scripts.  I seem to be missing some understanding about how the
> interface works.  Could somebody tell me how to fix this command below?
> 
>  
> 
> PyMOL>for x in range(10): cmd.label("(name ca and resi %d)" % x, "%s%s" 
> 
> PyMOL>% (resi, resn))
> 
> Traceback (most recent call last):
> 
>   File "/usr/local/pymol/modules/pymol/parser.py", line 232, in parse
> 
>     exec(com2[nest]+"\n",pymol_names,pymol_names)
> 
>   File "<string>", line 1, in ?
> 
> NameError: name 'resi' is not defined

You need quotes around the label expression '"%s%s" % (resi, resn)':

for x in range(10): cmd.label("(name ca and resi %d)" % x, '"%s%s" % (resi, resn)')

The expression has to be passed to pymol as a string to be interpreted
correctly.

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
<robert.campbell@...>    http://pldserver1.biochem.queensu.ca/~rlc