Locate a Nucleotide

• Type a position number into the Nucleotide Position text box and click “Go”. The nucleotide will be highlighted and the viewer will reposition itself if the nucleotide is out of view.
• Toggle between Crystal Structure numbering or E. coli numbering.
• Click “Clear” to clear selected nucleotide from map.

Navigate the Secondary Structure

• Zoom using the zoom slider.
• Drag the whitespace surrounding secondary structure to reposition the map.
• Status Box: Shows base type, crystal number and E. coli number (Ec) of current mouse-over nucleotide.

Freeze Tertiary Interaction Lines:

• Click a nucleotide to select it first. Right click on the nucleotide. Choose from:
• Freeze: Freeze tertiary lines associated with the selected nucleotide and mark that nucleotide.
• Unfreeze: Undo last set of frozen tertiary lines and marked nucleotide.
• Clear All: Clear map of frozen tertiary lines and marked nucleotides.

View links to other CRW Resources

• Click a nucleotide to toggle selection and the display of the information window. View:
  • Crystal number
  • List of basepairs and tertiary interactions
  • Links to basepair and base triple frequencies
  • E. coli number (Ec)
  • Link to basepair RasMol script
  • Link to Expanded Table View of information associated to the nucleotide
• "X" closes the window without unselecting the nucleotide.

View information about the secondary structure

• Click “Properties” to bring up the Properties tab.
• Legend: Legend for the current secondary structure.
• About: Information about the organism and the secondary structure version.

Print RNA Secondary Structure

• Click “Print” to print full secondary structure with current view settings.
• Tips:
• Use “Landscape Mode” for printing 23S structures.
• To print a specific area of the structure: right-click on whitespace > Print… (note: map may exceed paper size) or use Print-screen.

RNA Distances

• Mouse over a nucleotide to view 3D distances from the nucleotide to all other nucleotides. Click/Select a nucleotide to freeze or unfreeze distances.
• Select Distance Type:
• dWW: Distance between Watson-Crick and Watson-Crick faces.
• dCC: Distance between C1' and C1' atoms.
• dPP: Distance between phosphorus and phosphorus atoms.

• Set Maximum Distance.
• Click “Update” to apply changes.
• Distance Legend range will change accordingly.

Conservation Values

• Click a nucleotide to view its conservation values.
• Cons.3: Conservation values calculated over the three phylogenetic domains.
• Cons.A: Conservation values calculated over the Archaea (H. marismortui only).
• Cons.B: Conservation values calculated over the Bacteria (T. thermophilus only).

Motifs

• Click a nucleotide to view links to motif RasMol script (not available for all motifs).
• View E loop, E-like loop, GGA/GAA, UAA/GAN, C loop, LPTL, Tetraloops, K-turn, LUA@helix.ends, AA.AG@helix.ends, Tandem GA and H-turn motifs.
• Motif list is ordered by occurrence.

Basepair Groups

Basepair Conformations

Coaxial Stacks