Keywords: ProFit

Next: Miscellaneous Commands Up: ProFit V2.2 Previous: By-residue RMS Deviation

# Modifying the Fit

Normally, no weighting is applied during the fitting i.e. all atoms are weighted equally. The `WEIGHT` command causes the fitting to be weighted by the mean of the B-values in the equivalent atoms. Normally, you wouldn't use this with real B-values, but with some other weight parameter (e.g. SSAP scores).

The `BWEIGHT` command weights the fitting by the inverse of the mean of the B-values in the equivalent atoms. This is useful for genuine weighting by B-values (i.e. the mobile set atoms will be less heavily weighted).

The `NOWEIGHT` command switches off weighting.

Atoms can also be removed from consideration in the fitting and RMS deviation calculations using temperature factors as a cutoff. The `BVALUE` command allows you to specify a B-value cutoff and any atoms with B-values greater than this value will be ignored completely in both the fitting and RMS deviation calculations. The B-value may not be higher than this value in either the reference set or the mobile set. For example, if you specify 10, then atoms with B-values greater than 10 will be ignored.

By specifying a negative value for `BVALUE`, you require that any atoms with B-values less than the absolute value you specify will be ignored. For example, if you specify -10, then atoms with B-values less than 10 will be ignored.

The value may be followed by an optional `REF` or `MOB` parameter which restricts checking of B-values to the specified structure.

Next: Miscellaneous Commands Up: ProFit V2.2 Previous: By-residue RMS Deviation