Hi Scott, I made a ChimeraX recipe web page to show this transparency and shadows trick. https://rbvi.github.io/chimerax-recipes/shadows/shadows.html That's amazing Esther refound it in that long fitting video. Tom
On Feb 10, 2023, at 12:23 PM, Scott Stagg <sstagg@fsu.edu> wrote:
Thanks, Tom. That’s exactly what I was looking for! Esther Bullit found the video. It’s this one https://www.youtube.com/watch?v=v3jI43YJQMg Fitting an atomic model in an electron microscopy map with ChimeraX youtube.com Scott
On Feb 10, 2023, at 3:09 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Scott,
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.
open 1080 from emdb light soft volume level 0.6 open 1grl preset cylinders fitmap #2 in #1 transparency #1 80 material transparentCastShadows true lighting model #2 multishadow false graphics silhouettes true set bgColor white light full
Thanks for asking!
Tom
Opaque map, and transparent map, and transparent map with shadows with soft lighting.
<image1.png><image2.png><image3.png> 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.
<image4.png><image5.png><image6.png>
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 <https://urldefense.com/v3/__https://www.stagglab.com__;!!PhOWcWs!3QUvw8SGqeg...>
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