Inline Help

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Quick Start

First, please download the files to be used in this guide by right clicking on them and selecting Save As from the drop down menu. Be sure to remember where you save them - your Desktop is a good location: S.cerevisiae.ct S.cerevisiae.rnapredict.ct S.cerevisiae.mfold.ct. These files are, in order, the native fold of Saccharomyces cerevisiae, a prediction from rnapredict, and a prediction from mfold.

Now start the program by clicking the following link to jViz.Rna 2.0. To get started, load a structure or structures using the File menu. When the file chooser dialog pops up, you can select multiple structures by holding the Shift or Ctrl keys to select a block of files or add or remove individual files to the current selection. jViz.Rna can load files with .ct, .bpseq, .dbf, .dbn, or .dbn.txt extensions.

You can now choose which visualization mode you would like to use by selecting it in the View menu. Each view has its own small help text that appears along the right hand side of the screen. To show or hide the help text you can use the small arrows located in the vertical bar to the left of the text.

The left side of the screen contains the structure manager at the top, and the configuration options for each view at the bottom. Apart from the statistics and dot plot views in which you can select as many structures in the same group as you would like, each other view imposes a limit of two selections. To change the colour of the hydrogen bonds in displayed structures, click on the small coloured square to the left of the structure name.