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
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?