I'm not sure what video that is in. But there is some obscure ChimeraX magic involved. If you use the "soft" lighting (shadows cast from all directions) with a transparent surface it looks horrible because transparent surfaces by default don't cast shadows in ChimeraX. The reason for that default is often you are showing a molecule inside a transparent surface and then the molecule is dark (black actually) and hard to see. Because the transparent surface doesn't cast shadows it does not shadow itself so you don't get any of the darkened cavities that help 3D appearance. To make transparent surface cast shadows use ChimeraX command

material transparentCastShadows true

If you have an atomic structure (#2) inside the surface it will look black (shadowed), but you can tell it not to accept shadows

lighting model #2 multishadow false

The model inside can look pretty horrible and flat with soft lighting and you might try full lighting that adds a spot light, and also use silhouette edges.

Here is an example of all these tricks.

material transparentCastShadows true

lighting model #2 multishadow false

graphics silhouettes true

Opaque map, and transparent map, and transparent map with shadows with soft lighting.

Atomic model is dark inside transparent map casting shadows. Can make atomic model not accept shadows. "Full" lighting instead of soft can make the atomic look less flat.

On Feb 10, 2023, at 6:48 AM, Scott Stagg via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi everybody,

I’m writing because I saw in a YouTube video that you used “soft” lighting with transparency for an EM density map. It looked great. I can’t find the video again or the right documentation on how to do it. There was some command with the lighting that you typed in the command line. Do you know what I’m talking about?

Thanks,

Scott

Scott Stagg
Professor
Institute of Molecular Biophysics
Department of Biological Sciences

Florida State University
Tallahassee, FL 32306-4380
w: 850-645-7872
f: 850-644-7244
sstagg@fsu.edu
https://www.stagglab.com

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