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Scaling
The expected radius of gyration of
the embedded coordinates can be calculated from the complete matrix
of interatomic distances produced
for the embedding. This expected radius is often larger or smaller
than the radius of gyration calculated from the embedded coordinates.
Therefore, the
MMDG statement calculates a scaling factor equal to the ratio of
the expected to actual radii of gyration and declares
it to be the symbol $DGSCALE. The embedded coordinates should be
multiplied by this factor, because it makes subsequent regularization
easier.
Xplor-NIH 2025-03-21