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 http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html Tom

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