Since it was getting to be very messy trying to change one of the LogOptimizerStates every time I wanted different output, I wrote a new module for doing (graphical) output from IMP, called IMP.display. It provides abstractions for turning particles into geometry and writers to write the resulting abstractions as CMM, VRML or Bild files. Currently there are classes to generate geometry from XYZR particles and from bond particles. There is also a single LogOptimizerState class which subsumes both VRMLLogOptimizerState and CMMLogOptimizer state (which are now marked as deprecated).

Anyway, take a look at things and see what you think. I have added an example in fragments.