Added implementation for #293
Revised zero indexed in docstring.
Oops had hardcoded native.pdb
More docs, added atom_indices to ConvertDataToHDF
Forgot numpy import in ConvertData
Minor update to comment
Added iext flag for ConvertData
Fixed RebuildProject to use len(mdtraj.open())
Raise IOError if Rebuild cannot find the conformation file.
Merge pull request #299 from SimTk/rebuildproject

Fixed RebuildProject to use len(mdtraj.open())
Merge pull request #298 from SimTk/iext

Added iext flag for ConvertData
Merge pull request #294 from SimTk/atomindices

Added implementation for #293