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.