look at the GAP README file
look at the discom help file
go to the
GAP page
look
at the ddm_scripts README file
download
ddm_scripts (perl)
download
ddm_scripts (awk)
© Copyright 1995, Garry P. Gippert & Mikael Akke.
Last updated Feb 6, 1996.
The program 'discom' takes two different ensembles of PDB-formatted structures and calculates the mean and standard deviation of each distance difference between specified atoms in the two ensembles.
The resulting distance difference matrix (DDM) is very useful for analyzing structural changes, perhaps especially when the two ensembles of structures are similar and the changes are small and/or complex. The DDM makes it easy to identify just where the changes occur in the molecule, and typically aids in choosing which residues to RMSD superimpose in order to highlight structural differences. The DDM can also be directly visualized on the structure for this purpose. An advantage with calculating the ensemble average is that one directly obtains a statistical measure on which structural differences are significant.
Further details (equations and figures) and examples on the use of the DDM and various ways of visualizing it are given in my web poster on the DDM method.
In addition to the 'discom' program, we provide various scripts for turning
the output from 'discom' into a format suitable for input into
Mathematica (Wolfram Research) for
plotting of the matrices, and into
GRASP
(Anthony Nicholls)
for visualization of the distance difference "vectors" on the structure.
We also provide a bare-bones Mathematica notebook that examplifies
one way of reading the DDM into Mathematica and representing it as a color
coded matrix. In addition, sample GRASP macro files are supplied for
reading and displaying of the DDM on the structure.
The appropriate reference for the ensemble averaged DDM is:
Akke, M., Forsén, S., & Chazin, W.J. (1995)
J. Mol. Biol. 252, 102-121.
The DDM for comparison of two individual structures has been
presented previously:
Nishikawa, K., Ooi, T., Isogai, Y., & Saito, N. (1972)
J. Phys. Soc. Jpn.
32, 1331-1337.
discom is distributed as part of the GAP (geometry analysis programs, aka gippert's analysis programs) package, the non-discom parts of which are also well worth checking out.
Please send email to Garry Gippert if you download the GAP package and decide to use it. This way Garry can notify you when new versions and bug fixes are available.
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