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:

What are distance parameters?

Distances used in formatting a secondary structure graph:

How do I format a new helix?

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.