Protein least squares fitting form the command line

Sometimes I want to fit two (or more) PDB structures and, really, those times I want to just run the alignment and get the "modified" PDBs. For these cases, I don't need to run UCSF Chimera, Pymol or Swiss PDBviewer. For those cases I love ProFit:

ProFit is designed to be the ultimate protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc.

-Taken from the authors page.

Compilation is very very easy. If you have access to Intel compilers you can add these flags:

CC = icc -O3 -fast -parallel

and you can also use the 64 bits version of icc.

Regards!