NAcontacts is a perl script which will read a pdb file with hydrogens and write a table of contact information between nucleic acid bases in different layers.
NAContacts is a perl script which uses Probe to calculate a table of base-stacking areas and scores, either between base layers or between single bases. It operates on a nucleic acid PDB file with all H atoms (usually added with Reduce). To visualize the contacts quantified in the output table, look at the kinemage file that NAcontacts produces (or run Probe with “base” as the atom selection).
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NAContacts is free software available under the terms of its own BSD-style license.