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:

1. Adjust map opacity to 100%
2. Unshow and reshow anything (ambient lighting returns)
3. 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)

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

(pretty!)

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

(argh!)