Dear Andreas

  I ran into a similar problem more than two years ago when I wanted to fade one surface and bring in another one.  *But*, I thought the problem did not appear when you ray trace the image; are you implying the problem exists even in the ray traced image? Below is the query I sent, and Warren's answer to me:

I wanted to slowly fade in one surface while fading out
another. In other words, make one progressively less
transparent, while the other is made more transparent. It
turns out, unfortunately, that during the transition, the two
transparent surfaces affect each other adversely, and one
essentially blocks the other, even though they should be
transparent. This is shown on the second picture. The gray
surface is 20% transparent, and the salmon surface is 80%
transparent. The gray surface is fine by itself, but seems
"covered" in certain regions when the (mostly transparent)
salmon surface is present. In ray tracing, this seems not to
be a problem (see first picture...).


You've hit a limitation with PyMOL's OpenGL renderer: it can't currently do
a global Z-sort of all transparent triangles in a scene...just within a
single object.  This will be addressed eventually, but not soon.

Ray tracing with transparency_mode=1 is the only way to get proper
intersections of transparent surfaces.



On Apr 10, 2007, at 2:12 PM, Andreas Forster wrote:

Hey all,

I've run into the following problem while making some movies with MacPyMOL 0.99rc6.

I have a protein in surface representation that I start with transparency = 0 and a cavity (voidoo-created map) as surface with transparency = 1.  In other words, the protein surface is visible, the cavity is not.  When I cross-fade the transparencies, like so:

for i in range (1, 41):
   cmd.set ("transparency", i*0.025, "protein")
   cmd.set ("transparency", 1-(0.016*i), "cavity")
   cmd.png ("fadeOut_%02d" %i)

the protein disappears and the cavity appears gracefully.  However, those parts of the cavity hidden behind a wall of protein don't fade in as the protein surface disappears.  They only appear when the protein surface transparency has reached 1, and there is a sudden jerk between the second-to-last and the last image created by above script as the cavity becomes fully visible.  I remember that this issue has come up before but don't remember if there is a solution.  Could someone enlighten me please?


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Harry M. Greenblatt

Staff Scientist

Dept of Structural Biology 

Weizmann Institute of Science        Phone:  972-8-934-3625

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