repackseed(1)               General Commands Manual              repackseed(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 orig-
       inal 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 con-
       tour 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

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                 5.2.0                       repackseed(1)