[Chimera-users] tuning transparency of VDW spheres

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 15 09:05:19 PST 2010

Hi Boaz,
You can use transparent colors for atoms, bonds, ribbons, etc.  You could use the Color Editor or "colordef" command to create a transparent color and then apply it, or directly specify the color as R,G,B,A (where A = 1-transparency) in the "color" command.  However, there is no option analogous to the "single layer" surface setting, so it won't look as nice as transparent surface.  With ribbons, it can be reasonable if there aren't too many crossings of the ribbon segments, but with sphere atoms you see a bunch of intersecting slivers -- they aren't automatically pruned from the display.  Another difficulty is that you can't just specify keeping the same colors for the atoms or ribbons but making them transparent; each transparent color must be specified separately.

open 2gbp
show ligand
rep sphere
colordef tgray  .7 .7 .7  .5
color tgray C
color 1,0,0,.5 O


If you wanted to show sticks inside, probably the best way would be to open a separate copy of the structure and display it as sticks. 

Instead of showing transparent spheres with a separate copy as sticks inside, it would probably be better to make a surface that encloses just those atoms (see command "surfcat") and then make it transparent.


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 Nov 14, 2010, at 2:30 PM, Boaz Shaanan wrote:

> Hi,
> Is it possible to tune the transparency of the VDW spheres (as with surfaces for example)  if I choose to render some atoms as spheres and still would like to see the bonds (rendered as sticks)? Just wondering.
> I'm working with the 1.4 official release.
>    Thanks,
>                Boaz

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