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

---

ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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