RNA and DNA Secondary Structure Image Production


Secondary Structure Input:

ct          (Connect)
dbn      (Bracket)
bpseq  (Column)
rs          (Save file)
nts        (From json)

Paste your secondary structure input into the text area below:

Save File Output:

  Command/Ctrl-a to select all, then copy and paste to a local file for future use

Add Bonds:

  Enter a comma separated list of bonds, formatted with the Leontis and Westhof nomenclature

Color Input:

  Enter a space separated list of numbers to color bases on a gradient


RiboSketch Homepage
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What is RiboSketch?


Using the Program

Mouse Commands

Menu Features



Keyboard Commands



Adding and Deleting 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:
  1. sequences: semicolon-separated list of RNA or DNA sequence strings which are in upper or lower case respectively
  2. starts: comma-separated list of zero-based indices of the first residue of each sequence
  3. positions: semicolon-separated string of x,y,z positions of each residue. In the current version the z-values are set to zero.
  4. radius: the radius of the residues in pixel units
  5. backbone_distance: target distance of two residues that are adjacent in sequence
  6. basepair_distance: target distance of two base paired residues
  7. color_scheme: an integer that stands for the color mode
  8. outline: true/false indicating whether the residues are drawn with a black circle
  9. movement: true/false indicating whether the simulation mode is on
  10. labels: true/false indicating whether the residue labels are shown or not
  11. rigid_helices: true/false indicating whether rigidifying helices is activated or not
  12. rigid_loops: true/false indicating whether rigidifying loops is activated or not
  13. rigid_hairpins: true/false indicating whether rigidifying hairpins is activated or not
  14. relax_ids: comma-separated list of residues whose basepairs are not affected by forces
  15. display_order: residues are displayed in this order. This is useful in order to achieve foreground/background effects
  16. pair_table: residue partners for each base pair (-1 for unpaired bases). Similar to base pair column in a CT format file.
  17. non_canonicals: extra information about non-canonical base pairs
  18. base_colors: assignable colors for each base (comma-separated RGB values between 0 and 1)