-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Michael George Lerner
Sent: Saturday, November 20, 2004 12:23 PM
To: Seth Harris
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] RE: wire mesh spheres?
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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