How can I generate a movemap file, which seems
necessary for backrub operation?
I don't think that backrub requires a movemap - perhaps it's only necessary to backrub only part of the structure?
I've never used a movemap file before but it seems to be simple. The code is in src/core/kinematic/MoveMap.cc line 252 (init_from_file). It looks like the format is simple, just a sequence number and then a token for which degree of freedom is moveable (your choices are BB and CHI). Note that this sequence numbering is relative to 1 - it has nothing to do with the PDB numbering.