Viewing a structure

• Circle diagram
• Vienna format

Circle diagram

A. The "Always show residue labels" mode is off. B. The "Always show residue labels" mode is on. 1. Menu bar. 2. A diagram. 3. Residue labels

The "Circle diagram" dialog is used to display a structure as a circle diagram. Use the View>Circle diagram command on the Menu bar to display this dialog. The circle (Fig.A) contains the numbered nucleotides of the structure. Arcs connect nucleotides that form a complementary pair.

Menu bar commands
• File>Save to PS. Saves the current circle diagram as a postscript file.
• View>Always show residue labels. Displays the label for each nucleotide of a structure (Fig. B).

Vienna format

1. Selected nucleotides. 2. A nucleotide sequence. 3. A secondary structure.

The "Structure view" panel is used to view a primary structure and a bracket representation of a secondary structure. Use the View>Structure view command on the Menu bar to display this dialog. The upper panel displays the nucleotide sequence of a structure. The lower panel displays a secondary structure. Each pair of parentheses ... (..)... corresponds to a Watson-Crick (complementary) pair. The opening parenthesis represents the most 5' nucleotide of the complementary pair, the closing parenthesis represents the most 3' nucleotide of the complementary pair. The dot "." represents a nucleotide which is not paired.
The nucleotides that are currently selected on the Structure Graph panel are highlighted in blue.