[Chimera-users] Glassy surface in Chimera

Tom Goddard goddard at sonic.net
Tue May 8 08:35:16 PDT 2012

Hi John,

   Glass surfaces show reflections and also refraction (bending) of 
light passing through the surface.  Chimera does not do either of those 
two effects.  So Chimera surfaces never look like glass.  But here are 
the 3 most important Chimera settings for making a nice looking 
transparent surface.

1. Transparency.  Make a map surface transparent using the color button 
below the volume dialog histogram, click the "opacity" button, and 
adjust the A value which is opacity.  Or use the volume command, for 
example, "volume #0 color .7,.8,.9,.7" specifying red, green, blue and 
opacity values on a scale of 0 to 1.

2. "Glossy" lighting.  Use menu Tools / Viewing Controls / Lighting and 
change Quality from "normal" to "glossy".  This gives nicer specular 
highlights (bright spots) on the surface calculating them per-pixel 
instead of per surface triangle vertex.  This option may not be 
available with very old graphics cards.

3. Silhouette edges and white background.  Black edges on your surface 
with a white background make the depth easier to perceive.  Enable that 
with commands "set silhouette" (or menu Tools / Viewing Controls / 
Effects) and "set bg_color white" (or menu Actions / Color / All Options).

   I've attached an example image made with these commands:

open emdbID:1962
volume #0 color .7,.7,.7,.5 level 1
set bg_color white
set silhouette
open 4a0w
rainbow chain
~rib ~:.A,.M

See the image tutorials in the Chimera manual for more ideas



> Hello,
> I am trying to show a density map as a glassy surface within which 
> various molecular chains have been fitted.   Can anyone please tell me 
> how to produce such a glassy surface for the density map in Chimera?
> Thanks,
> John Squire

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