Re: [PyMOL] Making transparent boxes with colored surfaces?

Wed, 23 Apr 2008 11:11:05 -0700 

Hi Tsjerk,
It works Great! Thanks so much. I'll have to study your code to see where I was going wrong. 

Dean

On Apr 23, 2008, at 10:39 AM, Tsjerk Wassenaar wrote:


Hi Dean,

Funny, really. Last week I was just playing around a bit with creating
boxes in pymol, e.g. to create a bounding box, and I wanted to have it
transparent. So here's a script, giving you a function 'rect', which
takes two tuples, specifying the far edges of the box:

rect( [x0,y0,z0], [x1,y1,z1],name="box",rgbt=[1,1,0,0.5])

The rgbt argument specifies the color and transparency. Feel free to
go through the code to see how things are done (although you won't
hear me say it's perfect). In case you have any suggestions, also feel
free to contact me, either on or off list.

I hope it helps. Cheers,

Tsjerk


On Wed, Apr 23, 2008 at 5:22 PM, Dean Waldow <wal...@chem.plu.edu>  
wrote:

 Hi Folks,


I am very new to pymol and have been learning a lot about using  
(mac)pymol.
However, I seem to be unable to make a box which is transparent  
and has
color. I have been able to make a box with the *.py script below  
but when I
do the ray tracing to get a nice image the box turns to grey /  
black. I have
also been able to to make prolate and oblate spheriods using ideas  
from the

pymol wiki.


My eventual goal is to have about three slabs or boxes with  
spheroids at the
interface of these slabs and my pdb results from a monte carlo  
simulation
where the spheriods highlight the changes in shape of my  
copolymers at the

interface.


Has anyone succeeded in making colored transparent boxes? Or might  
there be

another strategy?

Thanks,

Dean Waldow


Here is the script (modified from one that makes a bounding box I  
believe)

that makes my current solid box which turns grey with I issue the ray
command:


from pymol.cgo import *
from pymol import cmd
#
# SEGMENT     1
box = [
   LINEWIDTH, 1.0,
   BEGIN, VERTEX,
   COLOR, 0.0, 0.0, 0.0,

# Face 1
   VERTEX,   55.000,   55.000,   55.000,
   VERTEX,   55.000,    5.000,   55.000,
   VERTEX,   55.000,    5.000,    5.000,

   VERTEX,   55.000,    5.000,    5.000,
   VERTEX,   55.000,   55.000,    5.000,
   VERTEX,   55.000,   55.000,   55.000,

# Face 2
   VERTEX,    5.000,   55.000,   55.000,
   VERTEX,    5.000,    5.000,   55.000,
   VERTEX,    5.000,    5.000,    5.000,

   VERTEX,    5.000,    5.000,    5.000,
   VERTEX,    5.000,   55.000,    5.000,
   VERTEX,    5.000,   55.000,   55.000,

# Face 3
   VERTEX,   55.000,   55.000,   55.000,
   VERTEX,    5.000,   55.000,   55.000,
   VERTEX,    5.000,   55.000,    5.000,

   VERTEX,    5.000,   55.000,    5.000,
   VERTEX,   55.000,   55.000,    5.000,
   VERTEX,   55.000,   55.000,   55.000,

# Face 4
   VERTEX,   55.000,    5.000,   55.000,
   VERTEX,    5.000,    5.000,   55.000,
   VERTEX,    5.000,    5.000,    5.000,

   VERTEX,    5.000,    5.000,    5.000,
   VERTEX,   55.000,    5.000,    5.000,
   VERTEX,   55.000,    5.000,   55.000,

# Face 5
   VERTEX,   55.000,   55.000,   55.000,
   VERTEX,    5.000,   55.000,   55.000,
   VERTEX,    5.000,    5.000,   55.000,

   VERTEX,    5.000,    5.000,   55.000,
   VERTEX,   55.000,    5.000,   55.000,
   VERTEX,   55.000,   55.000,   55.000,

# Face 6
   VERTEX,   55.000,   55.000,    5.000,
   VERTEX,    5.000,   55.000,    5.000,
   VERTEX,    5.000,    5.000,    5.000,

   VERTEX,    5.000,    5.000,    5.000,
   VERTEX,   55.000,    5.000,    5.000,
   VERTEX,   55.000,   55.000,    5.000,

   END
   ]

obj = box

cmd.load_cgo(obj,'segment',   1)



--


--------------------------------------------------------------------- 
---


Dean Waldow, Professor               (253) 535-7533

Department of Chemistry              (253) 536-5055 (FAX)

Pacific Lutheran University          wal...@chem.plu.edu

Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/


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---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/>  
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623<rect.py>


--
------------------------------------------------------------------------
Dean Waldow, Professor               (253) 535-7533
Department of Chemistry              (253) 536-5055 (FAX)
Pacific Lutheran University          wal...@chem.plu.edu
Tacoma, WA  98447   USA              http://www.chem.plu.edu/waldow/
------------------------------------------------------------------------
---> CIRRUS and the Chemistry homepage: <http://www.chem.plu.edu/> <----
------------------------------------------------------------------------
























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