pdb2mp manual
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/)
