
Usage:
    java chiropraxis.mc.HelixBuilder [-flags] file.pdb [> output.kin]

HELIXBUILDER is an aid for finding helices in PDB files as well as N caps and
reporting certain information about them that may comprise evidence for back-
rubs at certain positions, e.g. the N cap.

Options:
    -kin
	Outputs a kinemage format visualization of helices and (opt'l) N caps.
	Alternative to -print.
    -print
	Outputs csv format information about helices and (opt'l) N caps.
	On by default.
    -ncaps
	Turns on opt'l N cap analysis.
    -onlyhbncaps
	Reports as N caps only those residues that are a Ser/Thr/Asn/Asp and 
	  make a sc Hbond to i+2 or i+3 mc.
	Works on both -print and -kin output.
	Also turns on opt'l N cap analysis equivalently to -ncaps.
    -smoothaxes[=#]
	Smooths DAK's local helix axes, one per residue in a helix, by
	  averaging each with its immediate neighbors the given number of
	  times (default: once). Multiple rounds of smoothing leads to 
	  straighter local helical axes that are less affected by subtle
	  local changes in helix direction.
    -verbose || -v
	Prints extra information you probably don't even wanna know...
    -append
	If doing kinemage output, don't print the @kinemage at the top.
	
