Set defaults for molecule display?
Hi, Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation. I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible? Cheers Oli
Hi Oli, There aren't "New Molecules" preferences (like Chimera has) in ChimeraX currently, sorry. Maybe one of the programmers can advise on how to hard-wire it into the code. For the non-programmers: You can use "open" with "autoStyle false" to avoid the automatic styling of atomic structures, but then they just come up as white spheres. Automatic styling rules: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html> You can make a custom preset but you would still need to choose it from the menu or apply it via command in a separate step. So probably not any more convenient than making an alias and then using the alias. Presets and user-defined presets: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup> Aliases: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html> Cheers, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2023, at 3:15 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation.
I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible?
Cheers Oli
Oli, My OpenCommands plugin should be able to help with this. In the settings, you can create a list of commands (or Python code) that run when a model is opened. If needed, you can specify the commands only run for a particular file type (e.g. .pdb) or file name. To borrow from Elaine's answer, you can have it run the `preset` command when a model is opened. I know the boxes for typing in the commands can be a bit small, so it might be useful to just add them as a preset which then gets applied. OpenCommands can be installed from the toolshed. After installing the plugin, restart ChimeraX for the settings to be available. The toolshed page has a bit more info. Best, Tony On Fri, Sep 1, 2023 at 4:25 PM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Oli, There aren't "New Molecules" preferences (like Chimera has) in ChimeraX currently, sorry. Maybe one of the programmers can advise on how to hard-wire it into the code.
For the non-programmers:
You can use "open" with "autoStyle false" to avoid the automatic styling of atomic structures, but then they just come up as white spheres.
Automatic styling rules: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>
You can make a custom preset but you would still need to choose it from the menu or apply it via command in a separate step. So probably not any more convenient than making an alias and then using the alias.
Presets and user-defined presets: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
Aliases: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html>
Cheers, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2023, at 3:15 PM, Oliver Clarke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation.
I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible?
Cheers Oli
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Thanks Elaine! What I have done for now is to make an alias, and then use the very handy “buttonpanels” command to make a panel of buttons, including one for default molecule display: alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5 buttonpanel Shortcuts rows 3 columns 3 buttonpanel Shortcuts add default_disp command "default_mol_display" This does the trick nicely! Cheers Oli
On Sep 1, 2023, at 6:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There aren't "New Molecules" preferences (like Chimera has) in ChimeraX currently, sorry. Maybe one of the programmers can advise on how to hard-wire it into the code.
For the non-programmers:
You can use "open" with "autoStyle false" to avoid the automatic styling of atomic structures, but then they just come up as white spheres.
Automatic styling rules: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>
You can make a custom preset but you would still need to choose it from the menu or apply it via command in a separate step. So probably not any more convenient than making an alias and then using the alias.
Presets and user-defined presets: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
Aliases: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html>
Cheers, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2023, at 3:15 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation.
I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible?
Cheers Oli
Like this: https://www.dropbox.com/s/rcki801pyu0adkw/chimerax_custom.mov?dl=0
On Sep 1, 2023, at 6:43 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks Elaine!
What I have done for now is to make an alias, and then use the very handy “buttonpanels” command to make a panel of buttons, including one for default molecule display:
alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5 buttonpanel Shortcuts rows 3 columns 3 buttonpanel Shortcuts add default_disp command "default_mol_display"
This does the trick nicely!
Cheers Oli
On Sep 1, 2023, at 6:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oli, There aren't "New Molecules" preferences (like Chimera has) in ChimeraX currently, sorry. Maybe one of the programmers can advise on how to hard-wire it into the code.
For the non-programmers:
You can use "open" with "autoStyle false" to avoid the automatic styling of atomic structures, but then they just come up as white spheres.
Automatic styling rules: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html>
You can make a custom preset but you would still need to choose it from the menu or apply it via command in a separate step. So probably not any more convenient than making an alias and then using the alias.
Presets and user-defined presets: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets> <https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
Aliases: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alias.html>
Cheers, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2023, at 3:15 PM, Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
Is there anyway to set default preferences for molecule display? Currently it seems to vary (I think?) based on the number of atoms in the model - so relatively small proteins will load as ribbons, while larger ones will load in sphere representation.
I would rather set a default such that all molecules load as ribbons, rainbow colored by chain. Is this possible?
Cheers Oli
participants (3)
-
Elaine Meng -
Oliver Clarke -
Tony Schaefer