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NAME    
        analyze - calculate nucleic acid structural parameters
SYNOPSIS
        analyze [OPTION] [FILE]...
DESCRIPTION
        calculate various nucleic acid structural parameters (propeller,
        slide, roll, twist, backbone torsions etc.) from FILEs (stdin by
        default), and generate input to other utility programs.
        -c      output structural parameters between helical regions
                ("----" by default). The same effect can be achieved by
                directly modifying the input file (change "9" or "1" to
                "0" in the third column of each base pair list.)
        -h      this help message (any non-recognized options will do)
INPUT
        given a PDB file "sample.pdb", the input to analyze can be most
        conveniently generated with the utility program find_pair:
        find_pair -t sample.pdb sample.inp
EXAMPLES
        analyze sample.inp
        analyze sample1.inp sample2.inp sample3.inp
        find_pair -t sample.pdb stdout | analyze
        find_pair -t sample.pdb stdout | analyze -c
OUTPUT          
        sample.out, auxiliary.par, bp_step.par, bp_helical.par,
        cf_7methods.par, ref_frames.dat, poc_haxis.r3d, stacking.pdb
        hstacking.pdb
SEE ALSO
        find_pair, rebuild, frame_mol, ex_str, stack2img, cehs
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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