I think you're talking about the same thing I noticed .. if so, I asked
Warren about it and he said that it's on purpose; PyMOL only shows the
first transparent surface in order to make transparent protein surfaces
look less confusing/cluttered/distracting. If that's what you're seeing,
try
set ray_transparency, 1
and raytracing again.
-michael
--
This isn't a democracy;| _ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Sat, 20 Nov 2004, Seth Harris wrote:
Continuing on the transparency aspects of the original question...
When I ray trace Warren's recent example of transparent CGO's, it seems that
of the objects behind a given transparent one, only those that are fully
opaque show through the front one. That is, the spheres in the back get
blocked from showing through if they themselves have any transparency
setting. This gives a somewhat inconsistent appearance as the front sphere,
in this case, will look selectively transparent or opaque in different
regions. In case the words aren't clear, I took the example and put the blue
sphere in front so that the other three spheres, white, red, and green are
all partially hidden behind it, then do "ray". For me, only the white sphere
(which is opaque) shows through the blue one. I think I had noticed this
before, with non-CGO's too, so I was curious if it's a known problem or has a
fix?
I was going to test povray, but this reminded me that sphere transparencies
currently aren't passed on via make_pov to the povray input script, but I
know transparencies are honored by make_pov for other types of objects.
Perhaps a simple fix to have sphere transparency respected as well? Once I
manually edit the povray file to include the "transmit" keyword in the
pigment line the spheres do render as expected, with all three showing
through the front one regardless of each one's transparency.
-Seth
Warren's sample cgo code:
from pymol.cgo import *
from pymol import cmd
obj = [
ALPHA, 1,
COLOR, 1.0, 1.0, 1.0,
SPHERE, 0.0, 0.0, 0.0, 0.5,
ALPHA, 0.66,
COLOR, 1.0, 0.0, 0.0,
SPHERE, 1.0, 0.0, 0.0, 0.5,
ALPHA, 0.33,
COLOR, 0.0, 1.0, 0.0,
SPHERE, 0.0, 1.0, 0.0, 0.5,
ALPHA, 0.11,
COLOR, 0.0, 0.0, 1.0,
SPHERE, 0.0, 0.0, 1.0, 0.5,
]
cmd.load_cgo(obj,'cgo01')
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