Editing preset for initial colors
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
Hi Niels, Sorry, I don't know of a way to change the initial model colors currently. Hopefully in the future we could have something like the new-molecule preferences that were in Chimera. For now, maybe one of the other developers can advise where you can edit the hard-wired settings. Initial model colors: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html#autocolor...> Initial model colors are only a small part of the automatic styling that occurs based on the size, number of chains, etc. in an atomic structure: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html> You can circumvent automatic styling entirely by using "open" with "autostyle false" ... however, it will just show all the atoms as white spheres, which is probably not what you want: open 2gbp autostyle false One can define custom presets (see "Startup" preferences), <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> ... but in our parlance, a "preset" is a script applied to structures after they are opened, rather than rules defined before their opening. So you would always have to invoke the preset after opening the structure(s). Sorry about this limitation, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 20, 2022, at 9:03 AM, Niels Bradshaw via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@cgl.ucsf.edu> on behalf of Niels Bradshaw via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Sunday, February 20, 2022 12:03 PM To: chimerax-users@cgl.ucsf.edu <chimerax-users@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> on behalf of Niels Bradshaw via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Sent: Sunday, February 20, 2022 12:03 PM To: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (4)
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Anthony James Schaefer -
Elaine Meng -
Eric Pettersen -
Niels Bradshaw