Where Does ChimeraX Store Preferences and Sessions?
ChimeraX stores preferences per module in Application Support ChimeraX on Mac (~/.local/share/ChimeraX on Linux, AppData UCSF ChimeraX on Windows), with sessions saved as user placed .cxs files.
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ChimeraX splits user data two ways. Preferences live in a platform standard folder as one file per module, created only once you change something from defaults. Sessions are .cxs files you place yourself wherever suits the project.
That split keeps migrations simple. Copy the preferences folder for setup and the .cxs files plus their maps for work. Relative map paths inside sessions mean keeping session and data together avoids relink prompts on open.
Where ChimeraX stores this, by platform
%LOCALAPPDATA%\UCSF\ChimeraX
Per module preference files plus custom presets folder. Report exact path with info path user unversioned config. Sessions (.cxs) live wherever you save them.
~/Library/Application Support/ChimeraX
Same role as Windows prefs home for modules and presets. Session files stay with project data. Check the info command output when in doubt.
~/.local/share/ChimeraX
Linux variant of the preferences home. Keep .cxs sessions beside their maps for relative path resolution. Copy both halves for migration.
Frequently asked questions
How do I find my ChimeraX preferences folder?
Run info path user unversioned config inside ChimeraX to print the exact folder. The docs give this command because the path varies by platform and version. Preference files appear per module only after nondefault settings save.
How do I save a ChimeraX session?
Use File Save or save filename.cxs, keeping maps beside the session when possible. Sessions store map locations as relative paths when files sit together, so keep them in one folder. Reopening restores the full scene for figures and movies.
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