Eterna3D
Eterna3D is a feature that adds 3D RNA structures to certain puzzles. Additionally, players can add their own 3D stuctures to puzzles made in the Puzzle Maker.
Interpretation
Currently, the 3D structure should be interpreted as being the Target Mode structure and not the Natural Mode structure. As you switch between target mode and natural mode for the 2D structure, the 3D structure will remain in target mode.
Controls
The 3D window opens automatically and has three controls: Pan, rotate, and zoom. The 3D window can be resized, collapsed, and moved around the screen.
By default, clicking on the 3D window will pan the RNA structure; this default action can be changed between panning, rotating, and zooming using the settings (gear) icon on the 3D window. Additionally, there are some keyboard shortcuts that can be used to temporarily alter what clicking does: ctrl-click for rotating, shift-click for panning, and mouse wheel for zooming.
Hovering over a base on the 3D structure will highlight its location on the 2D structure. Individual bases or base pairs can also be mutated within the 3D window (in addition to on the 2D structure).
Puzzle Creation
Players can create their own 3D puzzles within the Puzzle Maker. At the moment, players can upload any 3D structure to any 2D structure as long as both representations have the same number of bases.
Here is a procedure for creating 3D puzzles based on specific, real-life 3D structures. This procedure works best with "simple" structures - more complex structures may require additional preprocessing in a program such as Chimera.
- Find a file containing 3D structure info for an RNA. Eterna3D currently accepts .cif and .pdb file types. There are various sites where 3D structures are publicly available:
- The RCSB Protein Data Bank (PDB) - Despite its name, this database does have structures besides just proteins. Some structures have just RNA, and some have RNA along with other ligands or molecules - the structures with just RNA are easiest to directly put into Puzzle Maker.
- RNA Central - This database focuses on RNA and contains data from a variety of other databases.
- Define the 2D structure within Puzzle Maker. This can be done either by using the toolbar buttons for adding/removing bases and base pairs or by altering the dot-bracket notation directly.
- Some databases will include dot-bracket notation along with the 3D structure. There also exist tools (such as RNApdbee) for predicting dot-bracket notation given a particular 3D structure.
- If the 2D structure has pseudoknots (denoted by characters such as "[]" or "{}" in the dot-bracket notation), you will likely want to use the NUPACK folding engine, which can handle pseudoknots.
- Upload the 3D file to Puzzle Maker. Clicking on the appropriate toolbar button will bring up a file upload window, where the correct file can be chosen. At this point, the Puzzle Maker will check if the number of bases is the same within the 2D structure and the 3D structure - if not, an error message will appear.
- Do a visual check to see if the 3D structure seems reasonable. Do the displayed bonds seem plausible? If not, revisit and edit the 2D structure.
- Solve the structure and submit the completed puzzle (similarly to other puzzle submissions).
History
Development of Eterna3D began in 2021. The feature was released in February 2022.
