[Chimera-users] .transparency in bild format

Tom Goddard goddard at sonic.net
Fri Nov 4 21:29:09 PDT 2011

Hi Keren,

   The BILD graphics rendering in Chimera daily builds is broken.  I get 
the same results as you where the specified color is not used and the 
transparency does not work.

   In the Chimera 1.5.3 production release the color works but the 
transparency works very poorly and this is a known deficiency (although 
not explained in the documentation).   In 1.5.3 I believe that 
transparency works by adding the color (red,green,blue) of your sphere 
multiplied by (1-transparency) to the image.  This is often very wrong.  
For instance if you show a transparent sphere on a white background it 
will be invisible -- you'll just see solid white.  The problem is that 
the stuff behind the transparent sphere is not dimmed.

   I suggest giving up on BILD if transparency is important and instead 
use a Chimera command file.  The following command will make a sphere 
with correct transparency.

     shape sphere center 0,0,0 radius 10 color 1,0,0,0.3 modelId #0

Put it in a file with a ".cmd" suffix.  If you want to make many spheres 
and have them be part of the same Chimera model then be sure to specify 
the modelId parameter.  Otherwise the spheres will end up as separate 
Chimera models.


> hello:
> I am trying to use the transparency option in the bild format.
> it seems that:
> .transparency 0.3
> .sphere 0 0 0 10
> results in a sphere
> however
> .color 1 0 0
> .transparency 0.3
> .sphere 0 0 0 10
> results in a black image, it only works if transparency is set to 0.
> any suggestions what i am doing wrong?
> thanks, keren.

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