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What is RiboSketch?
RiboSketch is a drawing program for the production of RNA and DNA secondary structure images.
The user provides an input file (.ct, .bpseq, .dbn, or the save file type .rs) containing the sequence and base-pairing of the strand(s).
Features
Works with multiple strands, non-canonical interactions, hybrid RNA-DNA base-pairing, pseudoknots, and interstrand interactions
Creates automatic layouts and circle diagrams
Dynamic simulation mode
Interactive editing is enabled through precise commands
The user may save the state of the program and load previous save-states
Actions may be undone and redone
Using the Program
Load a secondary structure file (you can add additional bonds and non-canonicals once in the program)
Default start state is the “Radial Layout”.
Mouse over the top of the screen to access the MENU and to view COMMANDS.
Mouse Commands
Click on (or drag a selection box over) bases to select them. Hold shift to multi-select or toggle the selection of bases.
Drag selected nucleotides to move them.
To select individual nucleotides, hold ALT/OPTION and click.
To select one half of a helix, you can either:
Select the helix, then shift click on the side you don't want to unselect it.
Click and drag a selection box over one side of the helix.
ROTATION: “m” rotates clockwise about the mouse cursor, “n” counterclockwise. Hold shift to rotate with a smaller angle.
Menu Features
Sliders
Base Size: Size of nucleotides
Bond Length: Distance between base-paired nucleotides
Chain Length: Effective only during simulation mode, controls distance between adjacent nucleotides
Color Scheme: “Pastel”, “White”, "Light", “Bright”, “Grey", and special ones:
Base Type: Each nucleotide type gets its own color
Rainbow: Each individual base gets its own color
Structure: Paired bases: Yellow, Unpaired: Blue
Custom: User must input number values corresponding to each base
Buttons
Save: Writes state of program into a text file (.rs), which can be loaded into RiboSketch.
Load File: Read a new secondary structure file into the program.
Load Bonds: Add new bonds from a text file of comma-separated entries with format: “firstID secondID bondType”
Example: 3 20 cWW, 4 19 tHS, 6 30 cSS
Load Colors: Color nucleotides based on a space-separated list of numbers (probing data) from a text file.
Radial Layout: Position nucleotides with the NAView algorithm, expanded to accommodate multiple strands and pseudoknots.
Circle Layout: Nucleotides are positioned in a circle with base pairs drawn as chords.
Simulation Mode: Apply forces.
Sim. Selected Mode: Only apply forces to selected nucleotides.
Rigid Helices: Enforce right angles for helices.
Rigid Loops: Circularize loops and straighten stems.
Rigid Hairpins: Circularize hairpin loops. Only has effect when Rigid Loops is OFF.
Zoom Reset: Return zoom to default.
Outlines: Toggle drawing circles around nucleotides.
Labels: Display numbering for every tenth nucleotide.
PNG Screenshot: Saves a screen image to the folder of the input file.
SVG Screenshot: Saves an SVG file of the screen to the folder of the input file.
Keyboard Commands
Editing
ROTATION: “m” rotates clockwise about the mouse cursor; “n” counterclockwise. Hold shift to rotate with a smaller angle.
"z": UNDO. Shift-Z to REDO.
"s": Turn on or off SIMULATION (forces)
"S": Toggle the SIMULATION MODE to apply forces to selected nucleotides only or all nucleotides.
“f”: FLIP the halves of a selected helix.
“x” or “y”: Flips the selected bases over the X or Y-axis.
"r": RELAX FORCES for selected nucleotides. Effective only in Simulation mode.
Display
+ / - : Zooms the screen in or out
0 : Resets the view scale
Arrows : When no nucletodies are selected, the arrow keys translate the window view.
1 / 2 : Brings the selected bases to the front or back, akin to Powerpoint
b / B : Base SIZE +/- (Same as slider)
o : Toggle OUTLINE
i : Toggle LETTERS
l : Toggle LABELS (Same as button)
k : View base number in secondary file
v : Toggle ANNOTATIONS (5' and 3', strand number)
c : Changes the color scheme of the nucleotides
p : Saves a PNG SCREENSHOT (Same as the button)
Adding and Deleting Bonds
Adding: Hold Spacebar, click first base, click second base.
Non-Canonical: Click "Load Bonds" button to add bonds with specified type through text input (Ex: 3 25 cWW, 8 12 tHS)
Deleting: Hold "d", click a base to delete its bonds.
The "RS" Data Format
The state of the program can be saved using the "RS" format (RS stands for RiboSketch), a special case of the Java Properties format: In other words, a text file in which keys and values are separated by an equals ("=") character. Comment lines (preceded by the "#" character) are allowed. Recognized keys are:
sequences: semicolon-separated list of RNA or DNA sequence strings which are in upper or lower case respectively
starts: comma-separated list of zero-based indices of the first residue of each sequence
positions: semicolon-separated string of x,y,z positions of each residue. In the current version the z-values are set to zero.
radius: the radius of the residues in pixel units
backbone_distance: target distance of two residues that are adjacent in sequence
basepair_distance: target distance of two base paired residues
color_scheme: an integer that stands for the color mode
outline: true/false indicating whether the residues are drawn with a black circle
movement: true/false indicating whether the simulation mode is on
labels: true/false indicating whether the residue labels are shown or not
rigid_helices: true/false indicating whether rigidifying helices is activated or not
rigid_loops: true/false indicating whether rigidifying loops is activated or not
rigid_hairpins: true/false indicating whether rigidifying hairpins is activated or not
relax_ids: comma-separated list of residues whose basepairs are not affected by forces
display_order: residues are displayed in this order. This is useful in order to achieve foreground/background effects
pair_table: residue partners for each base pair (-1 for unpaired bases). Similar to base pair column in a CT format file.
non_canonicals: extra information about non-canonical base pairs
base_colors: assignable colors for each base (comma-separated RGB values between 0 and 1)