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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
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