Changes this week: * A new writer, ChimeraWriter has been added which exports geometry to native Chimera constructs. It probably should be used instead of bild and cmm for most purposes as it combines the best of both types. * compose for transformation is now a free function so compose(rotation, vector) will work. * the geometry classes have been cleaned up and are now more consistent with IMP standards (and more likely to do what their names/comments suggest) * ParticleRefiner has been renamed to Refiner since the Particle was long and unnecessary.