[chimerax-users] Editing preset for initial colors

[Eric Pettersen]

Hi Niels,
	The initial model colors are defined in chimerax.atomic.colors as a list named atomic_color_names.  That list is:

	["tan", "sky blue", "plum", "light green", "salmon", "light gray", "deep pink", "gold", "dodger blue", "purple"]

You can use Python code to replace that list.  I have attached a Python file (start_colors.py) that replaces that list with ["khaki", "purple", "dodger blue"].  You could obviously edit the code to put in any color list you want.  Then you could put "open start_colors.py" in the list of commands that ChimeraX executes at startup (under Preferences/Settings→Startup) to have them always apply.  Just so you know, if you have N colors in the list, then the first N model IDs will get those colors.  For models with IDs higher than that, ChimeraX will try to use a color that contrasts with the colors in the list, the background color, and the selection-outline color (green).

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




> On Feb 20, 2022, at 11:00 AM, Anthony James Schaefer via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Niels,
> 
> There's a feature in my SEQCROW plugin that might do what you want. In the settings (Favorite/Preferences -> Settings... -> SEQCROW), you can define commands to run when a model is opened. It's not advanced enough to cycle through different colors for different models, though. 
> 
> Best,
> 
> Tony
> From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu <mailto:chimerax-users-bounces at cgl.ucsf.edu>> on behalf of Niels Bradshaw via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Sent: Sunday, February 20, 2022 12:03 PM
> To: chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu> <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>
> Subject: [chimerax-users] Editing preset for initial colors
>  
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
> 
> 
> Hi Elaine,
> 
> Is there a way in chimera X to change the initial colors preset for new models?
> 
> I’m not into the default tan color, so I end up changing the color immediately every time I open a new model.
> 
> In previous versions of Chimera, I had disabled color by model and set all new models to open with grey. In pymol, I defined the colors for the first 10 models I open in the startup script, which is even more convenient. Having the option to have the default to color by chain could also be nice if that is possible. I tried some workarounds like redefining the tan color, but it appears that is not allowed.
> 
> Thanks,
> Niels
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