Hi Ramy, Yes, ChimeraX applies some built-in rules to decide how to depict newly opened models, as described in Automatic Styling (Smart Initial Display) <https://www.cgl.ucsf.edu/chimerax/docs/user/autostyle.html>. There isn’t any built-in way to override these rules (other than to not apply them at all with the “autoStyle false” open command option). I can think of a couple of things you could do. Your alias could use the ”last -opened” atom specifier <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin> to apply your changes only to the most recently opened model (e.g. "hide last-opened atoms”). The other possibility is to use the excellent OpenCommands bundle <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxopencommands> to customize what happens when models of various types are opened. It is very flexible. Install it through the Tools→More Tools… menu item. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Jul 9, 2026, at 6:59 AM, Ramy Kazan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

When I open a large model (e.g., a ribosome) in ChimeraX, the default display style shows it as atoms in the spheres style. I’d like to change this so that, by default, all atoms are hidden, and the model is displayed as a cartoon only.

I’ve created an alias with the necessary commands and mapped it to a function key for quick adjustments. However, this approach has a limitation: after customizing one model (e.g., showing specific residues as atoms), opening a new model and using the function key overwrites the customized residues, applying the "cartoon-only" style to all open models.

There must be a setting to adjust this behavior, but I haven’t been able to find it. I also recall reading that ChimeraX treats small and large models differently—perhaps based on the number of chains or residues—but I can’t remember the exact rules.

Could someone point me to the correct way to set this as the default behavior for all new molecules?

Thanks for your help!

Best regards, Ramy _______________________________________________ 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/

Hey Eric, Thank you for both of your recommendations. I've been using the OpenCommands bundle for a month now, and it's exactly what I needed. Thank you very much! Ramy | From: "Eric Pettersen" <pett@cgl.ucsf.edu> | To: "Ramy Kazan" <ramy.kazan@ibpc.fr> | Cc: chimerax-users@cgl.ucsf.edu | Sent: Thursday, 9 July, 2026 20:05:04 | Subject: Re: [chimerax-users] Change default molecule display to cartoon only | (hide atoms) | Hi Ramy, | Yes, ChimeraX applies some built-in rules to decide how to depict newly opened | models, as described in [ | https://www.cgl.ucsf.edu/chimerax/docs/user/autostyle.html | Automatic Styling | (Smart Initial Display) ] . There isn’t any built-in way to override these | rules (other than to not apply them at all with the “autoStyle false” open | command option). I can think of a couple of things you could do. | Your alias could use the [ | https://www.cgl.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin | | ”last -opened” atom specifier ] to apply your changes only to the most recently | opened model ( e.g. "hide last-opened atoms”). | The other possibility is to use the excellent [ | https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxopencommands | OpenCommands | bundle ] to customize what happens when models of various types are opened. It | is very flexible. Install it through the Tools→More Tools… menu item. | --Eric | Eric Pettersen | UCSF Computer Graphics Lab || On Jul 9, 2026, at 6:59 AM, Ramy Kazan via ChimeraX-users || <chimerax-users@cgl.ucsf.edu> wrote: || Hi all, || When I open a large model (e.g., a ribosome) in ChimeraX, the default display || style shows it as atoms in the spheres style. || I’d like to change this so that, by default, all atoms are hidden, and the model || is displayed as a cartoon only. || I’ve created an alias with the necessary commands and mapped it to a function || key for quick adjustments. || However, this approach has a limitation: after customizing one model (e.g., || showing specific residues as atoms), opening a new model and using the function || key overwrites the customized residues, applying the "cartoon-only" style to || all open models. || There must be a setting to adjust this behavior, but I haven’t been able to find || it. I also recall reading that ChimeraX treats small and large models || differently—perhaps based on the number of chains or residues—but I can’t || remember the exact rules. || Could someone point me to the correct way to set this as the default behavior || for all new molecules? || Thanks for your help! || Best regards, || Ramy || _______________________________________________ || 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/