[Chimera-users] Chimera 1.11 - Combining Transparancies of Ribbon and Surface

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 1 11:44:38 PDT 2016

Hi Falko,
Thanks for the kind words!

With transparency, the default is to only show the topmost layer when there are multiple transparent layers.  You can turn off this single-layer setting, for example with command:  ~set singleLayer

Image tips, transparency:

However, the problem is that multiple transparent layers are often rendered incorrectly, with some objects blocking others even though they are supposed to be transparent.. the resulting appearance may not be satisfactory.  When I tried this with transparent ribbon inside of transparent surface, in some orientations part of the ribbon blocks another part of the ribbon instead of letting it show through.

Another approach is to show the surface as mesh (e.g. “surfrepr mesh”)  and the ribbon as transparent, but I agree it is not as nice as correct rendering of multiple transparent layers.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 1, 2016, at 4:36 AM, Falko Jähnert <falko.jaehnert at biochemtech.uni-halle.de> wrote:

> To whom it may concern,
> since I'm using Chimera a lot lately I enjoy the usage of this program and can't await the release of Chimera X. Now I like to ask if it is possible to combine the transparency of the ribbon and the surface representation using Chimera so that you can visualize both parts in varying transparency levels. My problem with this is if I use "transparency 80,r [Tag]" the part of my protein gets transparent (as requested) whilst activating the transparency function of the surface results in complete hiding of the previously chosen amino acids.
> Is there a workaround available?
> Thanks in advance for your help.
> Best regards,
> Falko Jähnert.

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