By default, PyMOL only shows the front-most transparent surface.
set transparency_mode, 1
to reliably combine all transparent surfaces in all displayed objects.
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From: [] On Behalf Of Andreas Forster
Sent: Tuesday, April 10, 2007 4:12 AM
Subject: [PyMOL] transparency cross-fading

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?