Thanks very much for the detailed info. Now I get some idea what I am looking at when the display comes up. Of course, your shadowed images are fantastic and very detailed. I could make some neat images from this. Always glad to help with the debugging. kas

Kenneth A. Satyshur, M.S., Ph.D.

Senior Scientist,

Department of Bacteriology: College of Ag and Life Sciences;

Departments of Bio Molecular Chemistry,

Neuroscience, Oncology, and Carbone Cancer Center:

School of Medicine and Public Health;

and the School of Pharmacy

University of Wisconsin-Madison

Madison, Wisconsin, 53706

608-215-5207

________________________________ From: Tom Goddard goddard@sonic.net Sent: Wednesday, May 27, 2020 11:44 AM To: Kenneth Satyshur kenneth.satyshur@wisc.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono

Hi Kenneth,

It occurs to me what probably caused the dark lighting you saw, since you said you do fitting. Mesh surfaces unfortunately look completely solid when using the ambient occlusion lighting that is enable by the soft and full lighting modes. That makes the structure inside either dim (for full lighting) or black (for soft lighting). This is a limitation of the ambient occlusion implementation which casts shadows from 64 directions -- it uses very coarse shadow maps that are too coarse se see the holes in the mesh.

The plan is to make meshes not cast ambient occlusion shadows, there is a bug report for that,

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3226

not hard to fix, but we are about to release ChimeraX 1.0 in a week and that requires a low level graphics change that is too dangerous to make just before a major release, so the fix is on hold.

One way to work around this is to make your mesh transparent, e.g. for 50% transparency command "transp #2 50". Transparent meshes in general I think look better than opaque. But mostly I would suggest not using soft or full lighting with mesh and atom stick displays. It just gives a bad result. Full lighting casts a sharp shadow and that makes the stick display look even more complicated and the shadow does not help at all. And the ambient occlusion of soft and full would ideally have almost no effect on stick and mesh since the scene is very sparse, but due to limitations of the algorithm it can make it look dark and smudgy. Full or soft are very good for surfaces or atom spheres -- space filling depictions.

Tom

On May 26, 2020, at 11:27 AM, Kenneth Satyshur <kenneth.satyshur@wisc.edumailto:kenneth.satyshur@wisc.edu> wrote:

Ok.stay safe there.

Get Outlook for Androidhttps://aka.ms/ghei36

________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Tuesday, May 26, 2020 12:30:14 PM To: Kenneth Satyshur <kenneth.satyshur@wisc.edumailto:kenneth.satyshur@wisc.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono

Try "camera sbs" and see if shadows look right. If they do look ok, but stereo does not then it will require some debugging with a stereo system that reproduces the problem and I am not able to test that until quarantine is over.

Tom

On May 26, 2020, at 10:01 AM, Kenneth Satyshur <kenneth.satyshur@wisc.edumailto:kenneth.satyshur@wisc.edu> wrote:

Thanks. I will check out the versions as they come out. Hopefully this can be fixed. I can try a VR and see what is up with the display if anything. kas

Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 ________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Tuesday, May 26, 2020 11:48 AM To: Kenneth Satyshur <kenneth.satyshur@wisc.edumailto:kenneth.satyshur@wisc.edu> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] 3D stereo lighting is not the same as mono

I made a bug report for this

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3315

I am not able to test stereo, don't have a computer that can do it. For me other two eye modes like VR and SBS (side-by-side) have correct shadows. The problem may be a graphics driver bug effecting shadow calculation. Or it might be a bug in ChimeraX in how OpenGL quad-buffering are used.

Tom

On May 23, 2020, at 4:39 PM, Kenneth Satyshur <kenneth.satyshur@wisc.edumailto:kenneth.satyshur@wisc.edu> wrote:

I am using version 1.0 in Centos7 with Nvidia 3D glasses and K4000 video card. I do all my work in 3D stereo. Especially density fitting. I noticed that the lighting is different in mono vs stereo mode. When i go to stereo mode with

camera stereo

the image is in stereo but the "full" lighting is on and the image is very dark with shadows. If I switch to 'simple' it is bright and has weak shadowing. Switching to 'soft' the image is flat black and can only be seen with white background but contains no atoms. I think this is a bug. But a Great improvement in rendering of images. thanks kas p.s. old chimera does stereo very well on my system Linux kenworkathome 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Kenneth A. Satyshur, M.S., Ph.D. Senior Scientist, Department of Bacteriology: College of Ag and Life Sciences; Departments of Bio Molecular Chemistry, Neuroscience, Oncology, and Carbone Cancer Center: School of Medicine and Public Health; and the School of Pharmacy University of Wisconsin-Madison Madison, Wisconsin, 53706 608-215-5207 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users