[chimerax-users] artificial lines or seems on surface using soft lighting

[Elaine Meng]

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 at 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