Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

REMAPMODEL(1)							 REMAPMODEL(1)

NAME
	repackseed - process seed model produced by transferfid

SYNOPSIS
	repackseed

DESCRIPTION
  This is a companion program for the shell script Transferfid.
  It is used to give the user a list of how points correspond between
  the original fiducial model and the new seed model, to repack
  the seed model to eliminate empty contours, and to produce a file with
  the coordinates of corresponding fiducials.  If it is given a file
  listing object and contour numbers for fiducials whose positions
  have been solved for in the first set, the list provided to the user
  will be correct provided that all of the seed points track.  Otherwise
  the lists could be wrong.  If a corresponding coordinate file is
  produced, no statements are made about the accuracy of the list and the
  user is informed that fiducials can be added or deleted as needed.

  Its inputs are:

  File name of original fiducial model for the first axis
  
  Name of file with X/Y/Z coordinates, as produced by Tiltalign, or
  Return if none available

  Name of new seed model for the second axis, produced by Beadtrack and
  stripped of points from the first axis
  
  Output file for final repacked seed model

  Output file for list of corresponding coordinates (Return for none)

  Section numbers (numbered from 0) for the best views in the original and
  in the second tilt series, and 0 or 1 for A to B or B to A transfer

HISTORY
  Written by David Mastronarde, 5/23/02
  Modified for corresponding coordinates, April 2006