============
INSTRUCTIONS
============

There are three available binaries of the program that perform the alignment:
   ALIGNMENT_DYN_32
   ALIGNMENT_DYN_em64t
   ALIGNMENT_DYN_mac
the first is compiled for 32 bit linux platforms; 
the second is compiled for Intel EM64T processor;
the third is compiled for Mac, and requires that ATLAS are installed.

To use the program, prepare the pdb files in a directory and give the following command:
   ALIGNMENT_DYN_??  <name pdb1>  <name pdb2>  <number of residues in correspondence>

Example:
   ALIGNMENT_DYN_32  1bba  1pgb  25

the number of residues in correspondence cannot be greater of the number of residues of the smaller protein.
Furthermore, the statistical relevance of the results as been tested for 70 or more residues into correspondence.


OUTPUT
======

For each pair of proteins compared, the program create a directory:
   output_<pdb1>_<pdb2>/
where the following files are produced:
   correspondence_<pdb1>_<pdb2>_R<number>.dat
   consensus_<pdb1>_R<number>.dat
   consensus_<pdb2>_R<number>.dat
   visual_<pdb1>_R<number>.pdb
   visual_<pdb2>_R<number>.pdb
   visual_R<number>.vmd
and many other files: visual_arrows_*.tcl

The file correspondence_<pdb1>_<pdb2>_R<number>.dat reports the performance of the alignment and the correspondence of the residues in the two proteins. The residues of each protein are numbered from 0, relatively to the order of residues in the input files.

The files consensus_<pdb>_R<number>.dat contains, for each protein, the consensus value of each residue. The residues are indicated with their resid ID and their chain label.
This consensus value gives the contribution of each residue in determining the alignment score.

In the visual_<pdb1>_R<number>.pdb the coordinates of the original pdb file are rototraslated in order to optimally superimpose (minimum RMSD) the aligned residues of the first protein with the corresponding residues of the second one, written in visual_<pdb2>_R<number>.pdb.
In these pdb files the aligned residues are marked, writing 1.00 in the column of the beta-factor, while the non aligned residues have 0.00.

To visualize the resulting alignment, a vmd load file has been generated by the program: visual_R<number>.vmd.
It visualize the two superimposed proteins, with the aligned residues in color.
The low-energy motions are also reported (10 modes for each protein), and they are represented as set of arrows.
The files visual_arrows_*.tcl are used by the vmd load file to draw the arrows.