artificial lines or seems on surface using soft lighting
Hi ChimeraX folks, When I used soft lighting, I saw lines/seams on the molecular surface (see the attached image). To reproduce this: ---------------------- load xxxx.pdb surface color violet lighting soft ---------------------- How to remove these artificial lines/seams? These lines also show up in the cutting plane in a section view. Many thanks in advance! Steve -- Steve Chou
Hi Steve, If you're going to zoom in that much, simple lighting may be better than an ambient-occlusion mode (soft or gentle). However, if you are sure you want to use one of those, bear in mind that the ambient-occlusion modes use various approximations like a finite number of shadowing directions, depth map size, and a depth bias value. Each of these parameters can be changed individually with the "lighting" command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> I see that the lines are more obvious with "gentle" lighting, but "soft" is prone to a sootier appearance especially viewed at such close range. Starting from "gentle" lighting, I was able to decrease the appearance of the lines by increasing the number of shadowing directions and the map depth, e.g. commands: lighting multishadow 256 light msmap 512 It's more difficult to avoid the sootiness of "soft" in this situation, without simply changing its parameters to be more like "gentle." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 5, 2020, at 1:52 AM, Steve Chou <stevezchou@gmail.com> wrote:
Hi ChimeraX folks, When I used soft lighting, I saw lines/seams on the molecular surface (see the attached image). To reproduce this: ---------------------- load xxxx.pdb surface color violet lighting soft ---------------------- How to remove these artificial lines/seams? These lines also show up in the cutting plane in a section view. Many thanks in advance! Steve
Hi Elaine, Thanks! Your suggestions (gentle lighting + commands) work well for me! Now the lines are almost invisible. All the best, Steve On Mon, Jul 6, 2020 at 12:28 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, If you're going to zoom in that much, simple lighting may be better than an ambient-occlusion mode (soft or gentle).
However, if you are sure you want to use one of those, bear in mind that the ambient-occlusion modes use various approximations like a finite number of shadowing directions, depth map size, and a depth bias value. Each of these parameters can be changed individually with the "lighting" command: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html>
I see that the lines are more obvious with "gentle" lighting, but "soft" is prone to a sootier appearance especially viewed at such close range. Starting from "gentle" lighting, I was able to decrease the appearance of the lines by increasing the number of shadowing directions and the map depth, e.g. commands:
lighting multishadow 256 light msmap 512
It's more difficult to avoid the sootiness of "soft" in this situation, without simply changing its parameters to be more like "gentle."
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 5, 2020, at 1:52 AM, Steve Chou <stevezchou@gmail.com> wrote:
Hi ChimeraX folks, When I used soft lighting, I saw lines/seams on the molecular surface (see the attached image). To reproduce this: ---------------------- load xxxx.pdb surface color violet lighting soft ---------------------- How to remove these artificial lines/seams? These lines also show up in the cutting plane in a section view. Many thanks in advance! Steve
-- Steve Chou
participants (2)
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Elaine Meng -
Steve Chou