[Chimera-users] displaying two surfaces

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 14 09:23:53 PDT 2009

Hi Marcus et al.,
You can see which surface model is "first" by looking in the Model  
Panel.  If you want the opposite order than what is listed in the  
Model Panel, just use the Model Panel to close the one that is listed  
first.  Then when you recreate that surface it will be listed below  
the other.

Example 1d86, with DNA (category main) and netropsin (category  
ligand).  Commands:

open 1d86
color yellow main
color red ligand
set bg_color white
surface main
surface ligand
surftransparency 50
start Model Panel

-- the red transparent surface is disappearing behind the yellow  
transparent surface, and the Model Panel shows the main surface  
listed above the ligand surface.  In the Model Panel, click the line  
for the main surface on the left and click the "close" button on the  
right (not the main "Close" button on the bottom!).

surface main

-- now the main surface is listed lower in the Model Panel and the  
red ligand surface shows through the yellow main surface

I hope this helps,

On Aug 13, 2009, at 6:05 PM, Thomas Goddard wrote:

> 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.
> 	Tom
> -------- 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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