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.