[Chimera-users] semi-transparent ribbon behind semi-transparent surface

Elaine Meng meng at cgl.ucsf.edu
Thu May 3 09:18:13 PDT 2012

On May 3, 2012, at 8:05 AM, Sumitro Harjanto wrote:

> Hi Elaine, 
> I used to use CHIMERA 1.5 to generate some molecular images. and I was able to show a "hint of shadow" of ribbon behind a semitransparent molecular surface. but I realised that I can no longer do that from Chimera 1.6 onwards. I have tried fiddling with the new "single layer transparency" value, but either option did not provide me with the visual effect that I could previously get in chimera 1.5. when I turned off the single layer transparency, the molecular surface became very messy with multiple shades and the color is visibly darker. but If I leave it on, the semi-transparent ribbon was not displayed at all. is there anyway that I can achieve a similar effect in Chimera 1.6? i.e if you're wondering what effect I am talking about here is an example: http://onlinelibrary.wiley.com/store/10.1002/emmm.201200213/asset/image_n/nfig004.jpg?v=1&t=h1rxtmm2&s=152573d22f1245472bbcb8ef11b0fcc757548517
> Thanks, Elaine!
> Cheers,
> Sumitro

Hi Sumitro!
In Chimera 1.5  each surface could have its own single-layer transparency.  Thus you could still have multiple transparent layers overall, but only the top layer of each surface.  I'm guessing the image is something like that (I don't have permission to view it).

In Chimera 1.6 the choices are only either a single layer of transparency, or all transparent layers.

In Chimera 1.5 if you turn off single-layer transparency for each surface, the result is the same as in Chimera 1.6 if you turn off global single-layer transparency.  However, I realize that does not help, since you don't want to show all layers (it's often ugly, as you describe). 

I don't know if there is any way to get exactly what you had before, but in 1.6 I suggest trying this:  use single-layer transparency (which is the default), make only the surface transparent, keep the ribbon opaque.  If you want the ribbon to be less bold, try making it a pastel color.

I am not involved in the graphics programming -- I CC'd the list since the other developers may have suggestions (and other users might find the discussion informative).
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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