GATHER_MAP
NCS Map Averaging Program
GATHER_MAP: NCS Map Averaging Program
This program is used to generate maps which have been averaged over the noncrystallographic symmetry. This operation is required when your model is being constrained to ncs and you are starting model building.
Like all constrained ncs in TNT, Gather_map is a little clunky. The script for running it must be edited for each project, and therefore not generic script is supplied. The prototype script can be found in tnt/doc/gather_map and will be described later. You will be required to calculate a separate map for each CLUSTER in your molecule. While on the graphics system you will need to remember to switch from one map to another at the proper time.
You cannot use ncs map averaging programs from other packages along with
TNT refinement. TNT's idea of noncrystallographic symmetry is more general
than all other programs in the field. Other programs define the transformation
as a rotation and a translation. TNT's ncs tranformation is generalized to
include a rotation, translation and a B factor shift. When an ncs averaged
map is calculated, the individual images must be rotated, translated, and
blurred or sharpen the appropriate amount. It does not make sense to average
two maps, one of a molecule with an average B of 20Å 
and another with an
average B of 40Å . The second map must be sharpened by 20Å prior to
being added to the first.