Query about system-wide ISOLDE installation

[Tristan Croll]

Query from Andrew Rabagliati at the University of Cape Town:

Tristan,

I supported the CCP4 2021 Workshop at Diamond 2 weeks ago.

I have a question regarding ISOLDE - I used to install it system-wide
on our servers at UCT, by dropping ISOLDE and its dependencies into
the ChimeraX python site-packages directory.

I had to delete users ~/.cache/ChimeraX and the toolshed/bundle_info.cache
to ensure it appeared, but I was fine with that.

Recently even that did not ensure ISOLDE appeared within ChimeraX.

Is this approach possible / sensible ?

Or is it best to have each student install from the Toolbox as needed ?

Cheers, Andy!

[Greg Couch]

On Linux and macOS, if you make the ChimeraX application files owned by a different user than root, then, as that different user, you can install bundles into the ChimeraX distribution. On Windows, you could need to change the ownership of ChimeraX to be a particular user (since ChimeraX is owned by a special system user by default), and install as that user.

To install a bundle, e.g., ISOLDE, you need to use the undocumented "userOnly false" option:

toolshed install ISOLDE userOnly false

or download the bundle and install it:

toolshed install ChimeraX_ISOLDE-1.1.0-cp37-cp37m-linux_x86_64.whl userOnly false

I'm looking into remove the restriction against being root, but

[Greg Couch]

but I'm more likely to make the Linux installers create and use a chimerax user. Not sure what to do for macOS users.

[Greg Couch]

For users, if you install the bundles before they first run ChimeraX, then there should be no problems. If they've already started ChimeraX, they will need to give the command:

toolshed reload installed

That will recreate the cached information.

Does that fix the problem?