How to annotate a drawing

There are many ways you can annotate your drawing:

Base numbering

You can add base numbers to a specific base in your structure, or to bases at regular intervals using the "Base numbers" entry in the "options" menu. Invoking this entry pops up the base numbering dialog. Try clicking on the button labeled "Add" to add a base number to the current base. Clicking "Remove" will delete the base number again. You can change the font and the distance of the base number to the base before adding the number again.

Clicking on the "go" button will add base numbers at regular intervals (given in the "Every" entry), starting from the "Number from base".

The numbers will move together with the structure. Their position relative to the base can be changed by dragging with the mouse.

Object configuration

Objects have properties such as fill and outline color and font. These can be changed to indicate special areas. Try this out by selecting a number of objects. If you want to select an object (or several objects) belonging to a structural element (such as a helix), without selecting the entire element, you will have to set RnaViz to "Select single objects" mode. Also remember that you can add or remove objects by Control-clicking.

Then activate the entry "Properties toolbar" in the "Objects" menu. This will show the properties toolbar. By default, the properties of all selected objects will be changed. Try this out by applying a different fill color.

You can adjust the selection first using the adjust selection dialog.

Tags are also worth a look, as they allow for an even more flexible (though somewhat more complicated) object configuration.

Drawing and linking

In RnaViz you can draw several types of objects (rectangles, text, lines, polygons and ovals). Drawing one of these objects is started from the "Mode menu". (They temporarilly change the way mouse and keybindings work.) These objects can be selected, moved, rotated and configured just like the objects constituting the structure. Dragging the top-left or bottom-right edge of a rectangle will change its size. Dragging an edge of a line or polygon will change the position of the edge instead of that of the entire object. Selecting the object and invoking the "Delete object" option in the "Edit" menu will delete the object.

These objects can also be linked to a certain base: Do this by selecting the object(s), and invoking the "Link object" entry in the "Objects" menu. You will then be prompted to select a base to which the object(s) should be linked. When the structure is being rearranged the linked objects will always maintain the same relative position to the base. This relative position can be changed by selecting and dragging the objects.

Boxes

Select a number of bases, then invoke the "Box bases" entry in the options menu. A box will be drawn around the selected bases. When the position of these bases is changed, the box will be redrawn as necessary.

Connections

Select a base, then invoke the "Connect bases" entry in the "Options" menu. You will be prompted for the base to which the previous base should be connected. Once you have selected this, a line will be drawn between the two bases. This line will be redrawn when the bases are repositioned. It can be configured using the normal properties toolbar

Clicking on the line and dragging will add an edge to the line, which can be repositioned (and deleted). The connection can be deleted by selecting it, and invoking the "Delete object" option in the "Edit menu".

Beads

Using the "Beads" entry in the "Options" menu, you can add a circular background to each base of your structure (like beads on a string). Invoking it will pop up the "Add beads" dialog box. From this dialog beads can be added to the selection or to the entire drawing. This dialog offers several options, e.g. to add beads of different size to the bases depending on their tags.