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)


-- 

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Dean Waldow, Professor               (253) 535-7533

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

Pacific Lutheran University          waldow@chem.plu.edu

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

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