Re: [PyMOL] transparency cross-fading

[Harry M. G. <har...@we...>]

BS"D

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...).


> Harry,
>
> 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.
>
> Sorry!
>
> Warren
>

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.ray
>    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?
>
> Thanks.
>
>
> Andreas
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Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology           har...@we...
Weizmann Institute of Science        Phone:  972-8-934-3625
Rehovot, 76100                       Facsimile:   972-8-934-4159
Israel