ProbKnot uses base pair probabilities determined using a prior partition function calculation to predict structures that can contain pseudoknots.
Predicting Pseudoknots in a Structure
- Click the button labeled "Partition Function Save File." A dialog box will open to get the name of a partition function save file (which may or may not contain pseudoknots).
- A default name is provided for the output ct structure file containing the predicted structure. This can be changed by clicking the "Output CT File" button.
- Change the number of iterations the calculation undergoes or the minimum allowed helix length for pseudoknots, if desired. The default parameters work best for most situations.
- Press the "Start" button.
- When the calculation is complete, a dialog box will open to ask if you would like the predicted structure draw on the screen.