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

  1. 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).
  2. 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.
  3. Change the number of iterations the calculation undergoes or the minimum allowed helix length for pseudoknots, if desired.
  4. Press the "Start" button.