How to draw a structure without using a skeleton

Introduction

You usually shouldn't have to draw a structure without using a skeleton. Example skeletons for most molecules are provided with the program in the examples directory. Even if you don't like our layout, it is better to start by creating the structure with one of with a skeletons given in the examples, rearrange that to the desired layout, and create a new skeleton from that. Structures drawn without skeleton will contain many overlapping regions.

You will need

a source file
First you will need a file which contains your sequence and information about its structure. This file can be in the DCSE alignment format (which usually has the extension .ali) or in the ct format (which usually has the extension .ct) as produced by the program mfold. These files do not HAVE to be made by these programs; any file with the same format will do. You can find some examples of these types of files in the directory examples.
WARNING: the secondary structure parser in RnaViz is somewhat pickier about the location of helix numbers in the DCSE alignment format than versions of DCSE <4, eg. the helix number must always come on a position after the helix opening symbol ([) in a sequence.

How to do it

clear the page
You can load several structures on one page: opening a new structure will not clear all existing drawings on the page. You can (but don't have to) empty the current page using the "Clear Page" option in the "File" menu before starting a new drawing.
open the source file
Invoke the 'Open' entry in the 'File' menu. This will pop up a file selection dialog which can differ depending on the operation system you are using. In this dialog, you can go through the file system hierarchy and select a file to be opened. If the file is in the DCSE alignment or ct format, RnaViz will recognise it, and create a structure drawing reflecting the structure in this source file.
Do not select a skeleton file
After you have selected a source file, RnaViz will imediately open another file selection dialog, from which a skeleton file can be chosen. Click on the "Close" or "Cancel" button if you do not want to use a skeleton. For larger molecules, not using a skeleton usually produces a not very pleasing drawing with lots of overlapping areas, which will take a certain amount of work to arrange properly. You should only do this if you really don't have a skeleton for the molecule; if you do have a skeleton for the molecule, even from a very distantly related organism, it will be better to use this a a basis for your drawing.
select the structures to be drawn
Some source files can contain more than one sequence with embedded structure information. When the source file only contains one sequence, this part is skipped.

When the source does contain more than one sequence, RnaViz will show a list with the names of the sequences in the file, and you can choose which have to be drawn. If you select more than one structure to be drawn, another dialog with 2 options will pop up. This will let you select wether all selected structures are drawn on the same page (Load selected structures on current page) or each structure is made on a seperate page, and saved to a different file. In the latter case RnaViz will prompt for a filename on which the names for these files will be based.

edit the structure produced
If you have just created a large structure without using a skeleton, it will probably look bad, with many regions overlapping. You can correct this by interactively rearranging parts of the drawing. For a badly arranged structure, this can take a while, but it is something you don't have to do often: Once you got one example arranged properly, you can create a skeleton from it, and use this to produce similarly aranged drawings. If you wish, you can also annotate your drawing by adding base numbers, labels, or colors.