[Chimera-users] Color surfaces

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 8 15:35:30 PST 2013

Hi Hernando,
I just tried the following and it worked:

(1) color atoms (opaque unless you actually wanted them to be transparent)
(2) select atoms,  use Color Zone
(3) Ctrl-click to select surface
(4) use menu: Actions... Surface... transparency [...]

That makes the whole surface transparent.  If you want different transparency levels for the different atoms, then you have to color the atoms with transparency.  For example, I could make tyrosines transparent white with command:

color 1,1,1,0.5 :tyr

...and then select atoms and then use Color Zone.  Each zone's color and transparency should match that of the corresponding atom.  If you prefer interactive coloring over commands, you could generate the desired transparent color in the Color Editor, then select the atoms you want to have that color and apply the color with menu: Actions... Color... from editor.

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

On Jan 8, 2013, at 3:23 PM, Hernando J Sosa wrote:

> Thanks Elaine that works, However I had a hard time setting the transparency. I tried selecting the atoms opacity colors but I didn't manage to made the surface transparent (neither the atoms).

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