[Chimera-users] Transparency of ribbons

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 3 12:06:46 PST 2008

Hi Luyuan,
Your question makes perfect sense (at least if I understood it  
correctly!) and in fact describes something I commonly want to do.   
However, I have only achieved a good result by saving images directly  
from Chimera, not raytracing.

See my example figures at

To make these, I did just what you described: used transparent colors  
for the ribbons and nontransparent colors for the side chains of  
interest.  That link has a little more information about how the  
figures were made.  You can save very high-resolution figures with  
smooth edges without raytracing; the difference will be that  
raytracing produces shadows and usually makes things look more shiny.   
You can try making objects look more shiny in Chimera (without  
raytracing):  choose Tools... Viewing Controls... Shininess, move the  
sliders.  In my experience, however, this makes the nontransparent  
things look more shiny and has very little effect on the transparent  

Maybe the others can say something about why transparent raytraced  
ribbons look dark, or offer suggestions about improving the raytraced  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 3, 2008, at 10:48 AM, lvyuan zhang wrote:

> Hi all,
>        I'm a new user and my question maybe a little weird to you  
> guys. I want to make some parts of my protein, let's say "A",   
> partially transparent, so when compared to other parts of the  
> protein, let's say "B", these "A" parts are hardly visible (the  
> background is white). So I set the alpha value of "A" to less than  
> 1, such as 0.1. then I save the image with POV-ray. The resulted "A"  
> is too dark, and it is still quite "visible". Is there any way to  
> make partially transparent ribbons lighter, instead of darker than  
> non-transparent ones?
>      I would really appreciate it if any one can help resolve this  
> problem. Thans!
> Cheers!
> Luyuan Zhang

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