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MatrixPlot 1.2: pdb2mp manual

Introduction Data format User matrix Mutual Nucl Mutual Prot Dist matrix

Inform pdb2mp MatrixPlot zoom


pdb2mp
NAME
pdb2mp - computes all the interatomic distances for a sequence with a set of three-dimensional coordinates.
SYNOPSIS
pdb2mp [options] pdbfile|colfile
DESCRIPTION
Can compute the interatomic distances between C-alpha or P atoms listed in a PDB file or in a "column" (col) file containing a set of coordinates. The output is written to stdout and is given in the "distance matrix" version of the mp format. pdb2mp can take input from a file or stdin. pdb2mp is written in nawk. When executing the program on a PDB file there are no options. When executing on a col file the options are to specify which columns the data are to be read from.
OPTIONS
comp=y|n
Print out all matrix elements including the complementary elements rather than just the upper triangle of the matrix.
When using a col file only:
xcol=<number>
Number. Specify the column where the x-coordinate is listed. Default is 5.
ycol=<number>
Number. Specify the column where the y-coordinate is listed. Default is 6.
zcol=<number>
Number. Specify the column where the z-coordinate is listed. Default is 7.
acol=<number>
Number. Specify the column where the residue or nucleotide symbol is listed.
scol=<number>
Number. Specify the column where an assignment is to be encoded as a bar along the edges of the plot (e.g., protein secondary structure).
EXAMPLES
To execute on PDB file
pdb2mp comp=y pdbfile > data.mp

Run on a col file

pdb2mp xcol=3 ycol=4 zcol=5 acol=2 scol=6 colfile > data.mp
AUTHORS
Hans Henrik Stærfeldt, hhs@cbs.dtu.dk and Jan Gorodkin gorodkin@cbs.dtu.dk.
Man pages by Jan Gorodkin, April 1999.
REFERENCE
MatrixPlot: visualizing sequence constraints. J. Gorodkin, H. H. Stærfeldt, O. Lund, and S. Brunak. Bioinformatics. 15:769-770, 1999. (http://www.cbs.dtu.dk/services/MatrixPlot/)



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