SUPERIMPOSE

DESCRIPTION
   superimpose all selected structures

GENERAL:
   display backbone only:  a toggle to let you view only 
       backbone atoms.

RMSD CALCULATIONS:
   superimpose on which structure:  this is the base 
       structure, the one which all others will 
       be superimposed to.
   superimpose on which atoms:  select the atoms to 
       superimpose onto, using the same selection syntax 
       as pymol.  You may choose from a pre-defined list, 
       or write your own.
   residue range:  enter range of residues to fit to (no spaces)
       eg. 20-88,90-99   eg. "all"
   backbone definition:  use only when printing out backbone statistics
   pairwise fit to mean:  if selected, when doing per residue rmsd's,
       first each entire protein will be fitted to the mean, then
       the residue rmsd's will be computed.  Otherwise, no extra
       fitting will be done before the residue rmsd's are computed.
	   Note: This is not used when calculating the best range.

CALCULATE BEST RANGE:
   Calculate the best residue range to use in superimposition.
   This takes all of the values from the FIT/RMSD section into 
   account when calculating the range, except for the backbone
   definition (used only for the statistics), and the
   "pairwise fit to mean" option


CMD USAGE:

   nmr_cmd.superimpose(superimpose_on_struc, which_atoms, 
   string_of_all_objects, range, data_directory, stop_at_rmsd)

example:
   nmr_cmd.superimpose('aria_1', 'C N CA', 'aria_1 aria_2 aria_3 aria_4',
   '22-88', '/home/leigh/data', 1.0)

   will superimpose all selected objects (structures)
   onto aria_1, using atoms c,n,ca and residues 22-88.
   when global rmsd is less than 1.0, calculations will stop.

