[PyMOL] Generate Surfaces from a dot cloud

[Mad]

Hi,

I'm looking for a possibility to do a surface triangulation for molecules, where I have basicly given only surface 
points. Is this possible with pymol or can you point me some sources for doing this. I did some searching through the 
scientific world and came across several triangulation algorithms and libraries but unfortunately I'm not a 
mathematician nor a big programmer so that I didn't see the possibility to easy use them for molecule surfaces.
After some thinking I recognized that there are several opensource molecular modelling programs out there and as I do 
not want to reinvent the wheel I ask this here.


Mathias

Re: [PyMOL] python for loop with pymol command usage

[Robert Campbell]

Hi Louis,

* Clark, Louis louis.cl...@codexis.com [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?
 
  
 
 PyMOLfor 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: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc