Fix issue #330 #352
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Fix issue #330 #352
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This PR closes #331. It is another attempt at the same logic, which (for some reason) doesn't cause the previous CI failure seen in the other PR. It also includes a small bug fix for the reference system modifications in the AMBER process. I had forgotten to create a local copy of the private object, so there was an attribute error when accessed.
Also closes #350 by replacing the example mapping visualisation with the new plot.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]