MatrixPlot 1.2: Distance matrices

Introduction

Data format

User matrix

Mutual Nucl

Mutual Prot

Dist matrix

Get a distance matrix of an RNA or DNA sequence with 3D coordinates. You can submit the sequence with its 3D coordinates by pasting it in, or read it from a file. You can also type a PDB entry name with corresponding chain identifier. After return of the matrix plot you can zoom around in it. For publication of results, please cite

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/)

Submission by pasting the sequence:

Give PDB entry (and chain):
OR
Type in the sequence with 3D coordinates: (data format description)



pdb2mp column format options: (Ignore if you are using PDB format)

xcol:

ycol:

zcol:

acol:

scol:

MatrixPlot options:

Title:

Title: size toffsetx toffsety

Color scale (interval R G B) 4 1.00 0.00 0.00 10 1.00 0.40 0.00 20 1.00 0.90 0.00 30 0.60 0.90 0.10 40 0.20 0.70 0.10 50 0.00 0.30 0.10 60 0.00 0.45 0.50 70 0.00 0.20 0.60 85 0.00 0.00 0.40

Color scale out: Yes No Colorgrain: No Yes Spacing: Color: size xcoloff ycoloff Grid: thickness xgridsize ygridsize

Show max distance:	Yes No	Position numbers: size xnumpos ynumpos
Secondary structure bar	Yes No	Structure bar: barthick xbarpos ybarpos
Sequence letters	No Yes	Sequence letters: scale xbarpos2 ybarpos2
Complementary matrix elements (cout):	No Yes
Reverse horizontal direction (xreverse):	No Yes	Reverse vertical direction (yreverse):	No Yes

Submission of a file containing the sequence:

Give PDB entry (and chain):
OR
Read the sequence file with 3D coordinates: (data format description)



pdb2mp column format options: (Ignore if you are using PDB format)

xcol:

ycol:

zcol:

acol:

scol:

MatrixPlot options:

Title:

Title: size toffsetx toffsety

Color scale (interval R G B) 4 1.00 0.00 0.00 10 1.00 0.40 0.00 20 1.00 0.90 0.00 30 0.60 0.90 0.10 40 0.20 0.70 0.10 50 0.00 0.30 0.10 60 0.00 0.45 0.50 70 0.00 0.20 0.60 85 0.00 0.00 0.40

Color scale out: Yes No Colorgrain: No Yes Spacing: Color: size xcoloff ycoloff Grid: thickness xgridsize ygridsize

Show max distance:	Yes No	Position numbers: size xnumpos ynumpos
Secondary structure bar	Yes No	Structure bar: barthick xbarpos ybarpos
Sequence letters	No Yes	Sequence letters: scale xbarpos2 ybarpos2
Complementary matrix elements (cout):	No Yes
Reverse horizontal direction (xreverse):	No Yes	Reverse vertical direction (yreverse):	No Yes

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GETTING HELP

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