Removing global rotations-translations using selected atoms for fitting

If the structure contains flexible parts then things can go bad : the least squares superposition algorithm will try to minimise the discrepancy across the whole molecule and will happily move the stable part of the structure away from its correct position (as long as the final rmsd is minimised). There are two solutions :

1. Completely ignore the flexible parts by throwing them away (this is the wrong solution).
2. Keep all atoms in the PSF and DCD files, but for the superposition use only atoms from the conserved structural core (this is the correct procedure).

The correct procedure can be implemented with xplor, vmd or carma. The carma way is to produce an ASCII file containing the indeces of the atoms that should be used for the superposition (much like the index file used for catdcd). The atom indeces are zero-offset (start from zero). Give this file the name fit.index. Then run carma with the flag "-index" :

carma -v -fit -ind CA.dcd CA.psf

The rms deviations reported by carma will be those calculated for the selected atoms alone (and not the whole molecule).