Difference Matrix

difference_matrix 1.1
---------------------
REQUIREMENTS: VMD Version 1.7 or greater 
 (new version uses uses lsort now instead of TclX luniq)
DESCRIPTION:
	This makes a matrix of all center of mass distances between
	the individual residues of two proteins. It saves the
	output to a file in the format
		residue_id1 residue_id2 distance
	The input options are:
		sel1 -- the first set of atoms to compare (the
		 reference atoms)
		sel2 -- the second set of atoms (the comparison atoms)
	 filename -- the output file name (the default is "diffplot.dat")
 Because one will usually like to compare all the residues of
	two systems, a simple interface to difference_matrix is
	also included. This interface is called whole_difference_matrix
	and it takes as arguments the two molecule ids to compare.
	See examples below for usage.
PROCEDURES:
	difference_matrix - calculates the difference matrix between
			 the residues specified in two selections
	whole_difference_matrix - calculates the difference matrix
			 between the residues of two specified
			 molecules
EXAMPLE USAGE:
	If you have only two loaded molecules, then they will have ids
	0 and 1. Then the following computes the difference matrix
		whole_difference_matrix 0 1
	Suppose instead you wanted to be more specific; you want the
	distance matrix between segment A of the first molecule and
	segment QQ of the second. Then you'll have to use the atom 
	selection command, which is fully described in the VMD manual.
		set sel1 [atomselect 0 "segname A"]
		set sel2 [atomselect 1 "segname QQ"]
		difference_matrix $sel1 $sel2
	If you want the output saved to the file "output.matrix" then
	change the last line to
		difference_matrix $sel1 $sel2 output.matrix
	If you want to compute the difference matrix between the
	first and last frames of a protein after a complete MD trajectory
	has been loaded into molecule 4, 
		set first_frame [atomaelect 4 "protein" frame first]
	 set last_frame [atomselect 4 "protein" frame last]
	 difference_matrix $sel1 $sel2 trajectory_difference.dat]
 The final output file can be viewed using a plotting package
 such as Gnuplot. The sequence of commands to load the output in
 gnuplot is: 
 set parametric
 set data style points
 splot "diff_matrix.data"
DOWNLOAD FILE:
	difference_matrix.tcl
AUTHOR:
	Andrew Dalke (dalke@ks.uiuc.edu)