ArcDiagrams
We will first need to load some CT files from the user's computer which we can then process with RNAStructViz. The procedure for doing this is illustrated in the schematically diagrammed screenshot of the application main window shown below:
In order to compare two structures in the same arc diagram, they must have the same underlying sequence. Generally, we think of a specific sequence as corresponding to a particular organism, with the different structures on the sequence corresponding to the native structure and the results of different structure prediction algorithms.
Using this terminology, we need to select the organism we wish to analyze with RNAStructViz. RNAStructViz will automatically process the loaded CT files and sort them into folders based on the underlying sequence. We can select one of these folders by clicking on the appropriate button on the lower-left of the image above. Once we have selected an organism/folder, the right-hand side of the application will be populated with the available CT structure files.
Note that, at any point, choosing a new organism button on the left-hand-side (as we just did) will allow us to consider graphical visualizations of a new set of loaded CT structures. The menu of new options is shown below:
Once you have the right-hand-side list of menu options displayed successfully, click on the Diagram button near the top of the right half of the window.
This will bring up the separate Diagram Window which is again schematically depicted in the image below:
