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/