ChimeraX aligns starting models to only one output model.

[tomgoddard]

For visualization ChimeraX aligns the starting models to the first output model of the first model group and only shows that output model superimposed with the starting models initially. Often there are multiple output model groups, for example, the exosome.cif has 4 model groups each with a best scoring model. Currently there is no way to have ChimeraX realign the starting models to an output model shown by the user. There is only one copy of each starting model.

The purpose of aligning the starting models to the output is to see how much the output model differs from the starting models. Also the starting models sometimes are at atomic resolution while the output model are at residue level resolution (e.g. nup84, exosome, mediator) and so the starting models show more detail which may be of interest.

I'm not sure how how to handle this user interface need. I could add a command that would do the alignment but few users would figure that out. Currently opening IHM data in ChimeraX provides no special graphical user interface -- it just displays the hierarchy of models in the Model Panel. Some more custom graphical interface seems to be needed but I do not have a design or even a draft of ideas of what functionality that user interface would provide. Usually in ChimeraX we have been developing the user commands before graphical interfaces and that is probably the best course here.