Automatic and manual controls for selecting mapped chains for superposition

When PDB structures involving multiple chains mapping to a single sequence are imported, it becomes ambiguous which parts of each PDB file should be used as landmarks for performing a superimposition.

Typically, one would only use the first 'best' set of chains in a given structure covering distinct parts of each sequence in the alignment. This would ensure that the number of columns used for the superimposition is maximised, and that conflicting cases are avoided (where eg chain A and chain C from pdb1xyy are both used to superimpose a structure onto a single homolog chain pdb1xyzB).

In some cases, the 'best chain' heuristic may not be what the user wants. Then, it should be possible to select specific chains by selecting them from the list of available mappings, as presented via a dialog box.