RNAstructure
Version 5.1
Copyright 1996 - 2010
by David H. Mathews
ProbKnot
ProbKnot takes the results of a partition function calculation and uses them to predict pseudoknots in a structure. Since ProbKnot is built to predict pseudoknots, the image results generated are always circular structures, whether or not pseudoknots are actually predicted in a given structure.
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 putative pseudoknots. 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.
- Press the "Start" button.