fithx directory:

	Programs to implement the "stepped-helix" method,
	A.H.Louie & R.L.Somorjai, 'Differential geometry of proteins;
	helical approximations', J.Mol.Biol. 168 (1983), p.143.
	The method fits each 5 successive alpha carbons to a helix,
	and from this determines from the helical parameters if the strectch 
	is an alpha helix, 3/10 helix, sheet (skinny helix), turn 
	(successive helix axes bend a lot), or coil.
	This was the first method I used to automatically assign secondary
	structure of proteins, originally as an aid in model building
	structures based on CAs fit to mini-maps, later for ribbon models
	as noted in Carson & Bugg, J.Mol.Graphics 4 (1986), p.121.

	The original code was FORTRAN source by JMR, revised by HRD,
	acquired from Steve Harvey who had obtained it elsewhere to fit
	helices of nucleic acids.  He does not who the authors are.
	The code was modified for the "stepped helix" method by mc,
	and later converted to C by Archie Cobbs here at the CMC.
	

	fithelix program:

	fit each successive run of 5 C-alpha coordinates to a helix.

	fithelix < protein.pdb > fithelix.out


	ahelix program:

	produce a secondary structural assignment from 'fithelix' output.

	ahelix < fithelix.out > protein.ss


	these programs work together via UNIX pipes, e.g.:

	fithelix < prot.pdb | ahelix > prot.ss



	bestfits program:

	fit selected runs of residues in a pdb file to helices.

	bestfits helix.runs < protein.pdb > bestfits.out

	the 'helix.runs' file consists of lines with two integers,
	specifying the first and last CA in the list to be fit.
	( note:  the numbering is consecutive starting at one )


	The 'fithelix.out' and 'bestfits.out' are ascii files in the 
	same format.


	determining inter-helical angles:

	interhx < bestfits.out > interhx.out




	creating cylinders:

		copy the awk files in this directory, and modify to
	choose your favorite radius and color by changing the values
	of the variables in the BEGIN section.
	'hx_bond.awk'  -  creates ribbon *.bond file of a single color
	'hxdp_bond.awk'  -  creates ribbon *.bond file where each fit
		helix is broken into three bonds to mark the dipoles.

	awk -f file.awk < bestfits.out > helix.bond


	examples:

		in the ../tutor directory, the file 'cam.pdb' and the
	file 'cam_hx.runs' ( see also 'cam_ss.ss' for numbering ) were
	run through the 'bestfits' program to make 'cam_fits.out'.
	This file was the processed by the UNIX 'awk' language to
	create the file 'cam_dipole.bond' used in the ribbon demo.