The above figure shows a typical plot from DDMP. The difference distance matrix of ribonuclease mutant (1rbe) was subtracted from the difference distance matrix of ribonuclease (1rnv). The delta values are plotted with colors representing CA differences of -1.25 to 1.25 Angstroms according to the scale at the top. You may also plot one distance interval with black dots or two or five distance intervals with gray scale dots.

The program gives real values of the differences in matrices for the color option (file #1 minus file #2). The black or gray scale options give the absolute values of the differences.

DDMP was written by P.J. Fleming to incorporate a variable dot matrix output. Some of the subroutines from the program ddm_ca_ctr by C.E. Kundrot were used in ddmp. A discussion of difference distance matrices with references may be found in Richards, F.M. and Kundrot, C.E. (1988) PROTEINS 3:71-84.

Features of ddmp include:

• the dot matrix plot where the dots may be two shades of gray or colors to reflect ranges of distance differences
  
• a variable window of residue numbers may be plotted
  
• an ASCII output of the difference distance matrix
  
• up to 1000 residue comparsion

DDMP should work on most UNIX flavored machines that have a FORTRAN compiler (the code is old fashion FORTRAN77).
Download the distribution as a tarred archive file.
Unpack it (tar xvf ddmp.tar), and change to the new directory, ddmp.
Compile the source code (f77 -o ddmp ddmp.f) and move the executable to a binary directory in your path, etc .

To use DDMP do the following:

• Obtain two PDB coordinate files for comparison (Equal number of residues)
• In your working directory (where you have write permission), type:

ddmp

The program will prompt you for various file names and options.

Note: The range of residues to be displayed MUST be a multiple of 25.

Alternatively, you can use a command file to provide default names of the files and options. To do this edit the ddmp.in file appropriately.

Note: The range of residues to be displayed MUST be a multiple of 25.

Then type:

ddmp < ddmp.in

After running DDMP you may look at the ASCII file output or you may look at the postscript grapical output similar to the figure above. To look at the postscript file you may type the following:

ghostview ddmatrix.ps &

The program has been tested in a variety of modes but please double check that your output makes sense.

Bug reports to pat.fleming@jhu.edu will be appreciated.