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The RSR (real space refinement) menu is a useful tool when fitting
molecular models into electron density. The algorithms used have been
described by Jones & Liljas [6]. All the refinement options in the
RSR menu operate in a similar fashion. A volume is chosen around all
the selected atoms, including a wall of thickness 3.5 Ångstrøms,
say, on all sides. Only density within this box is considered. The program
will then build up a model density of all atoms inside the box. This model
density is then scaled to the observed density. The model density is now
subtracted from the observed density, and the difference map is
stored. This is to prevent atomic groups from entering into density
belonging to neighboring atoms. When a group is being refined, the model
density for that group is added back into the observed density. The user is
able to influence the scaling and subtraction at will.
The optimization algorithm moves the fragment a certain step along a
direction that improves the goodness of fit. When the fit gets worse, it
attempts to locate a new direction along which to move. The user
controls the step size and how many different step sizes to try.
The RSR_zone command should only be used when you have an
excellent map.