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.