The reason you get "operation not permitted" when ChimeraX tries to look in ~/Downloads/ChimeraX is because you have prohibited ChimeraX from accessing the ~/Downloads directory. MacOS asks in a pop-up window if you wish to allow each application to access Downloads, Desktop and Documents folders when the application first tries to use those folders, and it remembers your choice. You probably denied ChimeraX access to Downloads. To allow ChimeraX to access the Downloads folder go to your Mac system settings (under the Apple menu), Privacy and Security, Files and Folders, ChimeraX and enable Downloads (image below).

If you really don't want ChimeraX to access Downloads then you can fetch files without checking the ~/Downloads/ChimeraX cache directory using the "Ignore cached fetches" check-button in the Fetch By Id panel (shown from the Files menu). Or in the open command you can use the "ignoreCache true" option, for instance, "open 9sjf ignoreCache true".

On Aug 3, 2026, at 8:55 AM, Steven Brawer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

MacOS, ChimeraX 1.12

Is there a way to stop ChimeraX from looking in the ~/Downloads/ChimeraX folder when I run the open command?

When it does this, the log file always says the operation is not permitted and then I have to move the ChimeraX directory to trash, which gets annoying. It appears not to look in the ChimeraX folder consistently, but only occasionally. I do not understand this. It is mentioned in the "open" help file, but I don't see the answer to my question.

Thanks

Steve
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