#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp
UP	arb_edit4.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB	helixsym.hlp
SUB	toggle_secinfo.hlp
SUB	e4_options.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		Helix

OCCURRENCE	ARB_EDIT4/Edit/Reload Helix

DESCRIPTION	The 'SAI' (see LINK{glossary.hlp}) entry 'HELIX_NR' contains
		numbering of potential higher order structure elements. The
		paired 5' and 3' helix halves are indicated by identical
		numbers. The SAI entry 'HELIX' contains symbols ([<( and )>])
		indicating positions which usually are base paired. This
		information is used by the editor to check the sequences for
		(correct) base pairing. User-defined symbols indicating base pairing and
		mispairing are shown below the particular sequences.


SECTION FORMAT OF HELIX/HELIX_NR:

		When the 'HELIX/HELIX_NR SAI's are analyzed the following steps
		are performed:

		1. HELIX_NR contains the helix numbering. A helix number
                   is a number between 0 and 100 optionally followed
                   by one letter: e.g. 11a, 23g, 0i, 6, 23,

                   A helix number is valid from the position of the
                   first digit to the position just before the next
                   helix number.

			eg. 	.........1a.........23b.........
			.	.........|||||||||||............

                   The '|' symbols indicate the positions for '1a'

		2. All '<[{(' symbols in HELIX are replaced by '('
                   All '>]})' symbols in HELIX are replaced by ')'

                        eg.	...[<<[..]>>].. is the same as ...((((..))))..

		3. For each helix number 'HN' a temporary helix is created
                   that contains all '()' symbols of the 'SAI HELIX' at
                   all positions where 'HN' is valid.

                        eg. HELIX_NR	.....1a.....23b.......1a....23b.....
                            HELIX	.....[<<[...[<[.......]>>]..]>].....
                            -> 1a	.....((((.............))))..........
                            -> 23b	............(((.............))).....

		4.	The (usually) paired positions can simply be defined
			by recursively removing the innermost bracket pairs
			in the temporary helices:

			eg. HELIX_NR	.....1a.....23b.......1a....23b.....
				HELIX	.....[<<[...[<[.......]>>]..]>].....
				Pos	123456789012345678901234567890123456
				-> 1a	.....((((.............))))..........
				-> 23b	............(((.............))).....
				1a 9-23	........+-------------+.............
				1a 8-24	.......+---------------+............
				1a 7-25	......+-----------------+...........
				1a 6-26	.....+-------------------+..........
				23b 15-29 .............+------------+.......
				23b 14-30 ............+--------------+......
				23b 13-31 ...........+----------------+.....

NOTES		After inserting or deleting gaps in the whole alignment (ARB_NT/
		Sequence/Insert delete columns) the helix information has to be:

			1. Checked (inserting a '.' between '1' and '2'
                           destroys the original '12').

			2. reloaded using 'Reload Helix'


EXAMPLES	None

BUGS		No bugs known
