Make AlphaFold PAE plot coloring work even when residues deleted

[Tom Goddard]

If residues of an AlphaFold structure are deleted then the PAE plot cannot be used to color domains. It gives an error saying the number of residues does not match.

One idea to fix this is to make AlphaFold model remember the original residue indexes so that even if residues get deleted we can still use the PAE plots. I could add a residue attribute "alphafold_residue_index" when the alphafold command trims a structure. But this would not fix the case when the user opens an AlphaFold model directly and deletes some residues. Still may be worth handling the trim case.