[Chimera-users] Transparency of ribbons

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 4 11:09:29 PST 2008

I forgot to mention that older versions of Chimera may produce darker  
raytracing results.  The July 2008 production release (1.2540) has  
better lighting settings for raytracing than earlier production  
releases (Nov 2007, June 2007, ...).  I recommend using the  July 2008  
release or newer, if you aren't already doing that.

On Dec 3, 2008, at 12:06 PM, Elaine Meng wrote:

> 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
> <http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/convergent/convergent.html 
> >
> 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 things.
> Maybe the others can say something about why transparent raytraced  
> ribbons look dark, or offer suggestions about improving the  
> raytraced results.
> Best,
> Elaine
> -----
> 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
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> 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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