4DR3 2D representation

Shown here is a circular diagram generated using the FR3D annotations for 4DR3. The black circle represents the annotated chains. For some structures an airport diagram is provided. To draw it click the airport button. Structures without one have a disabled button.

Interactions

Interactions are displayed as arcs connecting nucleotides, by default only cWW interactions are displayed. The dotted arcs are long range interactions, there include things like pseudoknots. To display other interactions use the interaction controls to the right. Clicking on a interaction will toggle displaying all interactions of that family and ones near that family. So clicking on tWW shows all tWW and ntWW.

Motifs

In airport mode motifs are displayed by default. To hide them click the motif button. Internal loops are shown in a green box, hairpins in blue and 3-way junctions in yellow. Currently we only extract 3-way junctions, in the future this may change.

Modes

In the default select mode, click and drag to create a selection box. All nucleotides within the selection box will be displayed in a jmol window to the right. The selection box is dragable and resizeable.

In click mode, click on a interaction or nucleotide to display it in 3D. In addition, some information about the clicked element will be displayed below the jmol window. To switch to the click mode use the selection mode control. Hovering over an interaction will highlight it and the nucleotides that form it. Hovering over a nucleotide will highlight it as well as all intereracations it forms.