Hi Tony, Elie, If you are curious why ambient intensity 1.25 is the right value it is because the ChimeraX default material ambient reflectivity is 0.8 (= 1 / 1.25) as shown by the ChimeraX "material" command material <cxcmd:material>Reflectivity: 0.8 Specular reflectivity 0.3 Specular exponent: 30 Ambient reflectivity 0.8 Transparent cast shadows: false Meshes cast shadows: false Tom
On Apr 17, 2024, at 2:54 PM, Élie Lambert <elie.lambert@umontreal.ca> wrote:
Hi Elaine, Tom and Tony,
Thank you so much for such prompt replies! The ambient intensity setting was not something I had thought of, 1.25 is indeed right on the money. I have tested it and the actual rendered color is the exact same rgb value as my input.
I had forgotten the attachment as you noted, here it is for future reference if needed.
Thank you again for being so helpful.
Kind regards, Elie
From: Tony Schaefer <tony.schaefer.chem@gmail.com <mailto:tony.schaefer.chem@gmail.com>> Sent: Wednesday, April 17, 2024 17:41 To: Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> Cc: Élie Lambert <elie.lambert@umontreal.ca <mailto:elie.lambert@umontreal.ca>>; chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Re: Color accuracy in ChimeraX / flat lighting
Hello,
I played around with the ambient intensity quickly, and a value of 1.25 gave basically the same atom colors between ChimeraX and screen grab.
Best,
Tony
On Wed, Apr 17, 2024 at 3:36 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Elie,
There is always lighting in ChimeraX, flat lighting is lighting, without lighting the models would be black. In flat lighting the lighting "ambientIntensity" parameter I see is 1.45 and if I change it it changes the brightness of the colors. The lighting command with no arguments will tell you the settings
lighting Intensity: 0 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.45 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 0,0,0 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)
Then I can change the ambient intensity using
lighting ambientIntensity 1
I am not sure if any ambientIntensity value will reproduce the colors on screen with the same color assigned to the model.
Tom
On Apr 17, 2024, at 2:23 PM, Élie Lambert via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi all,
I wrote a script to color code individual chains of a structure based on fold change values. When I plug the resulting rgb values in ChimeraX, the colors that are rendered are off by quite a bit in some cases. Attached is an example demonstrating such a difference. On the left is shown the color provided for the selected chain, which shows correctly in the ‘Select color’ window as rgb(196,216,214). However the resulting structure rendered has a different actual color (rgb(227,251,248), as measured with eyedropper tool in Illustrator).
This variation is not consistent, colors with higher saturation are not impacted as much, but can still be a bit off. I am using flat lighting with depthcue off, which I believe should mean that no shadows could affect the rendering. I have tried providing colors in other formats such as hex with no difference. I just updated to ChimeraX version 1.7.1 which also did not help (Windows).
Please let me know if I am missing anything obvious. Thanks in advance!
Regards, Elie _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <ChimeraX_Colors_FlatLighting.png>