How do I format from scratch?
Use the "Format" panel in XRNA. Select the "Format New Structure" button.
Formatting from scratch involves entering the following information:
- primary structure information
- base pair information for helices.
- an indication of formatting distances.
- an indication of the 5' start nucleotide and the 3' end nucleotide XY positions.
See example How do I build e.coli_5S from scratch?
Select the "New Primary Structure" button. A popup window will appear to enter
sequence data with. Either type or cut and paste a sequence of
nucleotide letters into the white "Edit Primary Structure" text field or
read a sequence in from a text file by selecting the "Read" button. The "Read" button
open file dialog box defaults to looking for text files that end in a ".txt" extension.
After a primary sequence has been entered the popup window can be deleted without losing
the sequence information.
Select the "Set New Helices" button. A popup window will appear to enter
helix information with. New helices are either entered individually
by selecting the "Set New Helix" button or read in by selecting the "Read" button.
The "Read" button open file dialog box defaults to looking for text files that end in
a ".txt" extension. All helices are entered by entering the 5' most nucleotide number
of the helix, the nucleotide number that it base pairs with, and the length of the helix.
For example, a file containing the following:
2 67 5
10 60 4
80 90 2
is saying that nucleotide number 2 base pairs with 67 and starts a helix that is
5 basepairs long, etc. After the helix information has been entered the popup window can be
deleted without losing the information.
Enter numbers into the text fields labeled 5' X:, 5' Y, 3'X, and 3'Y. Alternatively
select the radio buttons for picking the 5' end or 3' end and left mouse click any
where in the edit window.
In the Format panel left menu select the button labeled "Set Format Distances." See
What are distance parameters?
for an explanation of the distance parameters. The default distance parameters are used often
and are a good place to start.
When primary structure information and helix information have been entered select the
"Run Format" button to display an automatically generated secondary structure graph.
Use the "straight helical runs" radio button to have all stacked helices format straight
if desired. Use the "center after build" radio button to automatically center the entire
structure.
Change any parameters and re-select the "Run Format" button as often as desired to obtain
an initial strucuture. Select a prefix name for the new structure by typing into the
textfield labeled "prefix name:". Go to the "Import/Export" panel to write out.
Go to the "Edit" panel to further edit the initial structure.