How do I format a new secondary structure graph?
All formatting is done within the "Format" panel of XRNA. Formatting refers to the
automatic generation of a secondary structure graph. This is currently done in
one of 3 ways:
- from scratch - enter primary sequence, base pair information, distance
parameters, then generate.
- from a template - generate a new secondary structure graph from a parent
secondary structure graph by using an alignment file.
- from postscript - generate a new secondary structure graph from an old
style XRNA output file ("*.ps").
Distances used in formatting a secondary structure graph:
- distance from one nucleotide to the next in a single stranded region
- distance from one nucleotide to the next in a base paired region
- standard base pair distance (Watson-Crick base pair)
- non-standard base pair distance (all other base pair types)
A new helix can only be formed with nucleotides that are currently not
base paired. Use "Unset base pairs" button in the "Edit" panel
to unset base pairs in a constrained region (currently only set
up for "rna helix" and "rna base pair" constraints), if need be.
In the "Format" panel select the "Format Helix" button. This will
bring up a pop up menu to allow for base pairing a helix. A helix
may be re-formatted to what ever the default distance parameters
are, or, simply base paired without any reformatting. Interactively
pick the corners of a potential helix, or type in the corner
nucleotide numbers (remember that a helix in XRNA is a contiguous set
of base pairs).
If formatting a single base pair helix then pick each nucleotide in
the base pair twice.
Try reformatting. If it is an undesirable result, then select the
"Undo last re-format" button. When a desired result is reached select
the "Accept Preview" button.
Make sure the "Format Hairpin" radio button is off unless sure that
helix ends in a hairpin, or undesirable formatting may occur.
The "clock-wise formatted:" label in the pop up menu will remind you
if the helix is right or left handed. Change by editing helix later
in the "Edit" panel.