I'm making some breaking changes to RMF files as part of a cleanup. I think they are all in obscure areas that no one is using yet, but I just want to make sure that no one is surprised: - bonds will be stored using a different scheme. As a result, existing bonds in the file will be ignored. Adding backward compatibility support for this would be pretty easy. - the API for storing/extracting bonds has changed (the old API is still there, just no longer documented and now deprecated). There is now a general purpose API for storing data related to tuples. - the way triangulated surfaces are store is changing (and triangulated surfaces from IMP aren't supported at the moment as I have not gotten around to updating it). It now uses the variable length entries rather than external hdf5 data sets - the way segments and cylinders are stored has changed

On the plus side: - you can now associate arbitrary data with any tuple of hierarchy nodes (at the moment, the tuple must have size <= 4). So you can store information about bonds, torsion angles, angles etc. - mesh surfaces that vary from frame to frame are now supported - external HDF5 data sets are not used - polylines and poly-cylinders are now supported