[MMTK] question about modes

[OMAR NABEEL ALY DEMERDASH]

Dear sir or madam,
Of course, in normal mode analysis MMTK undoes the mass-weighting of 
the eigenvectors, rendering them not orthonormal.  Therefore, would one 
simply transform a matrix V consisting of these non orthonormal vectors 
to recover the original orthonormal eigenvectors like so:

M^(-1/2)*V*M^(-1/2) ?  
Moreover, would the masses in M simply be the masses of the residues in 
the order in which they occur in the PDB file?
Finally, when converting the modes that result from use of the fourier 
basis to orthonormal eigenvectors, is there any other transformation 
other than mass-weighting that needs to occur?
Help is greatly appreciated!

Sincerely,
Omar Demerdash