How to draw a structure using a skeleton

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.

a skeleton file
You will also need a skeleton file. A skeleton file stores the general layout of a previously made drawing. This layout can be applied to your new structure. Several skeleton files (LSU, SSU and 5S rRNA, intron, tRNA) are provided with the program in the examples directory. The closer the new structure resembles the one from which the skeleton files was made, the better the resulting drawing, and the less work you will have 'beautifying' the result. For instance, if you want to make a drawing of a bacterial SSU rRNA, it's best to use the skeleton file 'examples/ssu/Ecoli.skl'. Where the structure of your bacteria differs from that of E. coli, the drawing might have to be rearranged (see further). When you want to make several drawings of related sequences, it might be better to first create a more group specific skeleton.

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.
select a skeleton file
After you have selected a source file, RnaViz will imediately open another file selection dialog. In this dialog, you can select the skeleton file you want to use.
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
The structure produced might need some editing. You can interactively rearrange parts of the drawing. If you wish, you can also annotate your drawing by adding base numbers, labels, or colors.