[chimerax-users] Transparency with soft lighting

[Tom Goddard]

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.


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 at 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 at fsu.edu
> https://www.stagglab.com
> 
> 
> 
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image1.png
Type: image/png
Size: 158878 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image2.png
Type: image/png
Size: 95432 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0007.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image3.png
Type: image/png
Size: 143404 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0008.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image4.png
Type: image/png
Size: 233369 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0009.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image5.png
Type: image/png
Size: 302455 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0010.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image6.png
Type: image/png
Size: 323438 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20230210/48c5eda2/attachment-0011.png>