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>
Sent: Wednesday, April 17, 2024 17:41
To: Tom Goddard <goddard@sonic.net>
Cc: Élie Lambert <elie.lambert@umontreal.ca>; 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> 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> 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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