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#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
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