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NAME    
        find_pair - locate base-pairs and helical regions
SYNOPSIS
        find_pair [OPTION] PDBFILE OUTFILE
DESCRIPTION
        locate base-pairs and helical regions given a PDB data file. Its
        output can be directly fed into analyze, cehs and Lavery's Curves
        program.
        -s, -1  treat the whole structure as a continuous single helix.
                Useful for get all backbone torsion angles
        -c      get Curves input for a duplex
        -d      generate a separate output file for each helical region
        -p      find all base-pairs and higher base associations
        -t      read also HETATM records [recommended]
        -z      more detailed base-pairing information in the output
        -h      this help message (any non-recognized options will do)
INPUT
        PDB data file
        One-letter options can be in either case, any order and combined
EXAMPLES
        find_pair -t sample.pdb sample.inp
        find_pair -pt sample.pdb allbp_list
        find_pair -c sample.pdb sample_curves.inp
OUTPUT          
        base-pair listing for input to analyze, cehs and Curves
        bestpairs.pdb, hel_regions.pdb, col_chains.scr, col_helices.scr
        allpairs.pdb, multiplets.pdb, mulbp.inp
SEE ALSO
        analyze, cehs, anyhelix, ex_str, stack2img
AUTHOR
        Written by Xiang-Jun Lu at Wilma K. Olson Laboratory at Rutgers
        Check URL: http://rutchem.rutgers.edu/~xiangjun/3DNA/
        Report bugs to <xiangjun@rutchem.rutgers.edu>
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