The default is that transparent surfaces do not cast shadows because usually that gives a better result in the common case where most of the structure is inside the transparent surface and the point of making it transparent is to see inside. But if you cast ambient shadows from the transparent surface then the structure inside will be entirely black and hard to see. The shadow casting is not sophisticated enough to partially shadow, so a transparent surface will cast a shadow as if it is 100% opaque. To allow some light through would require ray-tracing which is an entirely different technology for drawing graphics than what ChimeraX uses. Only with the latest graphics high-end graphics cards (e.g. Nvidia RTX 2080) has raytracing become possible at interactive speeds.

On Aug 31, 2019, at 9:53 AM, Sindelar, Charles <charles.sindelar@yale.edu> wrote:

PS: one more note is that after I destroy my nice rendering in ChimeraX v0.6 by unshowing and showing the PDB model, I can restore it by the following sequence:

Adjust map opacity to 100%
Unshow and reshow anything (ambient lighting returns)
Adjust map opacity to 80% (ambient lighting stays)

From: "Sindelar, Charles" <charles.sindelar@yale.edu>
Date: Saturday, August 31, 2019 at 12:44 PM
To: "chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu>
Subject: semitransparent volumes with ambient occlusion

Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward!

Here is a little request.

For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful.

What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off!

I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like.

I sure would like to have this option! I guess there must be some reason it is disabled?

Best, Chuck Sindelar

Opaque map + PDB (ChimX v0.6)
(pretty but the PDB is obscured)

<image001.png>

After adjust to 80% map opacity (ChimX v0.6)
(pretty!)

<image002.png>

After unshow/show PDB model (ChimX v0.6)
(argh!)

<image003.png>

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