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> 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

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