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Modifying the Fit

The commands described in this section make use of the temperature factor column as a 'flag' and are therefore not compatible with the BZONE command (Section 9.5).

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 up previous
Next: Script Files Up: ProFit Version 3.1 Previous: Obtaining Output
Andrew Martin 2010-09-28