First pass at a pure jmol interface

This is a pure jmol interface for the library. This does not use jmol tools to
laod things, but instead it will load a whole structure and let you work with
that. This is another way of working with the 3D structures and is probably
more helpful to coloring tasks and the like. However this can't do things like
show neighborhood and the like.
Add getChain and getNumber

These are two methods to get the chain id and number for a given nucleotide.
Currently these assume the person is using new style ids. Not the best
assumption really.
Bug fixes

This fixes a variety of bugs with using a pure jmol interface. In addition, I
have removed the build script method. It seems like it's unneeded.
Conditionally add zoom

We don't always want zoom, so we don't try to generate it otherwise.