Last Modified: Wednesday, 01-Jun-2005 09:32:38 EDT

DDMP -- Differences Distance Matrix Program

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). For example the distance between residue 42 CA and residue 66 CA in 1rnv is 18.51 A; the same distance in 1rbe is 19.56 A. So [1rnv - 1rbe] = -1.05 and the dot representing this comparison is red according to the scale shown.

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

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 on an sgi(The path is /srv/local/r4k/)

• to use the irix64 version type:
  

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

Note: The title to be displayed MUST be 40 characters or less.

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 type:

cp /srv/local/ddmp/ddmp.in .

and edit the ddmp.in file to suit.

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 &

Reports or publications based on this program should contain an acknowledgement in a form commonly used in academic research. Suggested citation information:

Difference distance matrix plots were produce using the DDMP program from the Center for Structural Biology at Yale University, New Haven, CT.

The latest version of DDMP may be downloaded from its new home at Johns Hopkins University.

Bug reports should be sent to pat.fleming@jhu.edu

Last Modified: Wednesday, 01-Jun-2005 09:32:38 EDT