Next: RSR_map
Up: The RSR commands
Previous: The RSR commands
This is a menu that enables the user to change some parameters and
options relating to the real space refinement. There are 2 possible
choices for the refinement method, the CONV method, which tries to
maximize the convolution product between observed and model density, and
the DIFF method, which tries to minimize the difference density.
Although the convolution product method biases the fit to place single
atoms on grid points, it is less sensitive to errors produced by scaling
the model to the observed density. It can therefore be used when the fit
to the observed density is poor. The effect of grid biasing is most
severe when fitting single atoms and is reduced by fitting residue
fragments.
- Autoscaling
- This is an option to turn on automatic scaling
of model to observed density. It is effective in most of the minor
menus in RSR. It may sometimes be advantageous to switch off the
autoscale option and use the manual scaling in RSR_scale
instead.
- Autosubtraction
- The user is permitted to switch
off the subtraction of model density from observed. This is not
recommended, but may be used with the CONV refinement method when the
scaling of densities is inaccurate.
- Nscan
- Set the
number of search scans in the refinement procedure. Typical value
is 5.
- Stepsize
- Set the size of the Nscan steps in
Ångstrøms/degrees.
Typical values are 1.0, 0.5, 0.25, 0.2, 0.05.
- Form_factors
- Defines the values A(o) and C, used
to transform a B factor to an atomic radius A, using the relationship from
[2]:
B = 4pi * ((C*A)^2 - A(o)^2)
Typical values are A(o) = 0.90; C = 1.04 for high resolution maps
(1.7--1.9Å) and C = 0.82 for medium resolution (2.4Å).
See the discussion on page 
.
- Irad
- Specify how many grid points over which the grid sums are
formed. Should be of magnitude 3 Ångstrøms.
These parameters are also used by the RS_fit command.
Next: RSR_map
Up: The RSR commands
Previous: The RSR commands