Index
About RNAstructure
Accuracy
Acknowledgements
Algorithm
Annotating a Structure
Asking for Help
Audio Playback
Breaking Pseudoknots
Bulge Loop Size
Calculating Stochastic Samples
Calculation Modules
Changing Temperature of Calculations
Constraint File Format
Creating a Sequence
CT File Format
DH Thermodynamic Parameters
DNA Menu
DNA Thermodynamic Parameters
DNA-RNA Thermodynamic Parameters
Dot Plot Appearance
Dot Plot Color Selection
Dot Plot Module
Double Stranded Bases
Draw Module
Drawing a Structure
DS Thermodynamic Parameters
Dynalign Dot Plots
Dynalign Thermodynamic Parameters
Editing a Sequence
Efn2 (Energy Function 2)
Enthalpy Thermodynamic Parameters
File Formats
File Menu
Folding Dot Plots
Forbidding a Base Pair
Forcing a Base Pair
Forcing Double Stranded Bases
Forcing Single Stranded Bases
Formatting a Sequence
Free Energy Calculation
Free Energy Thermodynamic Parameters
Generating Suboptimal Structures
Hard Constraints (SHAPE)
Help Menu
Image Output
Internal Loop Size
List File Format
Loading a Sequence
Making Suggestions
Maximum Expected Accuracy
Module List
OligoScreen
OligoScreen Thermodynamic Parameters
OligoWalk
OligoWalk Calculations
OligoWalk Modes
OligoWalk Results
OligoWalk Thermodynamic Parameters
Outputting Base Pair Probabilities
Overview
Partition Function
Partition Function Bimolecular
Partition Function Dot Plots
Plot Range
Postscript Output
Precision
Predicting Base Pair Probabilities
Predicting Pseudoknots
Prediction Modules
Printing a Structure
Probability Annotation
ProbKnot
Pseudo-Energy Constraints (SHAPE)
Pseudoknots
Publication Quality Output
Quick Access Toolbar
Read While Typing
Refold
Refolding Dynalign Calculations
Refolding Structures
Rendering a Structure by Direction
Report a Bug
Resetting Constraints
Restoring Constraints
Reviewing Constraints
RNA Menu
Saving Constraints
Sequence Entry Particulars
Sequence File Format
SHAPE Annotation
SHAPE Constraints
SHAPE File Format
Single Stranded Bases
Specifying Chemical Modification
Specifying FMN Cleavage
Stochastic Sampling
Support
Switching Between Structures
System Requirements
Thermodynamic Parameters
Toolbar
Using Calculation Constraints
Using OligoScreen
Using OligoWalk
Variable Menus
Viewing an Entire Structure
Zooming a Structure