[Chimera-users] displaying two surfaces

Thomas Goddard goddard at cgl.ucsf.edu
Thu Aug 13 18:05:59 PDT 2009

Hi Marcus,

  Unfortunately Chimera does not handle transparency correctly when 2 or 
more models are transparent.  Maybe there is a way to get your two 
surfaces as pieces of a single surface model which could have there 
transparency set and would display correctly, but I can't think how. 
Another trick that would help you is to make the yellow surface have a 
higher model number so it is drawn after the white surface.  With the 
yellow surface in front that will give more correct appearance as the 
white transparent surface won't overdraw the yellow one.  I guess the 
surface command is going to produce the same model number as the 
molecule for both surfaces.  Maybe creating the yellow one after the 
white one will control the drawing order.  If that fails you may need to 
save the 3 residues in a separate PDB and surface it so it can have a 
distinct model number.


-------- Original Message --------
Subject: [Chimera-users] displaying two surfaces
From: Marcus Carr
To: chimera-users at cgl.ucsf.edu
Date: 8/13/09 5:50 PM

> I am trying to create a figure that encloses three residues in a protein 
> in one surface and the rest of the protein in another.  I put the three 
> residues into one group using surfcat and the rest of the protein in 
> another.
> When I try adjust the surface transparency, the three-residue surface 
> all but disappears.  If I set transparency to 0%, I appears normal.  If 
> I increase it even to just 1%, it almost completely disappears.  It 
> looks like wherever this three-residue surface is inside the protein 
> surface, it only shows if the transparency of three-residue is set to 
> 0%.  All this is with the protein surface set to 50%.  I'm not sure 
> whether this list accepts attachments, but I put in screen shots of what 
> it looks like.
> marcus

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