FirstRunInstructions

Instructions for new users

First-run welcome dialog display

To get users up and running with RNAStructViz, the first time the application runs, it displays a welcome dialog of the following form:

This dialog can always be accessed again by clicking on the circled help (question mark) button at the top right of the left-hand-side main window pane. The dialog will display every time you start RNAStructViz until you turn off this behavior.

You can skip the instructions for copying structures to your home directory in the section below by using the "Copy sample structures to your home directory" middle button in the first-run dialog pictured above. When accessing the welcome dialog by clicking on the help button, you will also be able to view a quick-start tour of the features of RNAStructViz by clicking on one of the displayed buttons.

Copy sample structures to your home directory (manually with a terminal)

The middle button in the welcome (or help) dialog pictured in the section above will automatically copy sample structures to your home directory in most cases, thus eliminating the need for the manual terminal copying instructions given below. If you have already copied the sample structures to your home directory with this button, skip ahead to the next section.

The sample CT and DOT files shipped with RNAStructViz are available in ${INSTALLATION-PREFIX-DIR}/RNAStructViz/sample-structures/ (browse the files online). On Mac OSX (if you installed with our brew package), you can copy the structures into an easier to find location by running the following commands at your terminal:

$ cd ~
$ mkdir -p RNAStructViz
$ cp -R /usr/local/opt/rnastructviz/sample-structures ./RNAStructViz/
$ cd RNAStructViz/sample-structures
$ RNAStructViz

On Linux and other Unix systems (for users who ran sudo make install), commands to copy the initial sample structures into a working directory inside of the user's home directory are as follows:

$ cd ~
$ cp -r /usr/local/share/RNAStructViz ./
$ cd RNAStructViz/sample-structures
$ RNAStructViz

For users with a local install of RNAStructViz built from this git repository, you can find these sample structures by navigating to the cloned directory and running:

$ cd ~/RNAStructViz/sample-structures/
$ ../src/RNAStructViz

After you copy the sample structure files, re-run RNAStructViz, click the "Load Files" button in the left-hand pane of the screen, and then navigate to this new local directory to select input files to load with the application. Note that the dialog that appears is capable of selecting multiple files at once by holding down CTRL (on Linux / Unix) or SHIFT (on Mac) as in any other multi-file selection GUI.

Adding RNAStructViz to the Applications folder on Mac OS

This option is targeted only at Mac OSX users. If you installed RNAStructViz from source on Mac OS, run the following:

$ cd ~/RNAStructViz
$ cp src/RNAStructViz macos-application/RNAStructViz.app/Contents/MacOS/
$ cp -R macos-application/RNAStructViz.app /Applications/

If you installed RNAStructViz using the brew installer on Mac OS, run the following:

$ cp -R /usr/local/opt/rnastructviz/RNAStructViz.app /Applications/

The benefit of this procedure is that it gives you a quick-launch icon to run the application.

Adding RNAStructViz to your terminal path

Let's make an alias for this command so it's easier to find and use on the system:

(On Linux -- From source install method)

$ cd ~/RNAStructViz
$ echo "export LSAN_OPTIONS=\"detect_leaks=1\"" >> ~/.bashrc
$ echo "export MALLOC_CHECK_=3" >> ~/.bashrc
$ echo "alias RNAStructViz=\'$(readlink -f src/RNAStructViz)'" >> ~/.bashrc
$ source ~/.bashrc
$ RNAStructViz

(On Mac -- With brew install method)

$ cd ~/RNAStructViz
$ echo "export LSAN_OPTIONS=\"detect_leaks=1\"" >> ~/.bash_profile
$ echo "export MALLOC_CHECK_=3" >> ~/.bash_profile
$ echo "alias RNAStructViz=\'/usr/local/opt/rnastructviz/bin/RNAStructViz'" >> ~/.bash_profile
$ source ~/.bash_profile
$ RNAStructViz

(On Mac -- From source install method)

$ cd ~/RNAStructViz
$ echo "export LSAN_OPTIONS=\"detect_leaks=1\"" >> ~/.bash_profil
$ echo "export MALLOC_CHECK_=3" >> ~/.bash_profile
$ echo "alias RNAStructViz=\'$(greadlink -f src/RNAStructViz)'" >> ~/.bash_profile
$ source ~/.bash_profile
$ RNAStructViz

Now you can run the application by typing RNAStructViz at your terminal.

A tour of the features of RNAStructViz

What does RNAStructViz do?

• It loads structures in CT, NOPCT, DOT and several other standard formats. The loaded structures are then grouped into folders in the left-hand-side pane according to their common base nucleotide sequences.
• After selecting a sequence by clicking on its folder, the right-hand-side window pane is populated with a set of operations that can compare the different loaded structures.

Operations on loaded structures

After loading structures from file, users can then compare the structures for the selected sequence by performing any of the following operations:

• Generate graphical arc diagrams to compare the overlap in pairings between up to three structures at once. The arc diagram window also lets users zoom and select consecutive sequences of nucleotides to view in a radial layout viewer based on ViennaRNA.
• Compute comparative statistics among all structures for the given sequence given a reference structure.
• Directly view the secondary structure base pairings in our color-coded integrated CT-file-style file viewer (accessed from the lower right-hand-side buttons in the main window).
• Export loaded samples to CT and DOT Bracket file formats starting from any input file format RNAStructViz supports from the CT file viewer window.

Have more questions?

The RNAStructViz WIKI page hosted here on GitHub is an excellent reference. The right-hand-side navigation tabs in your browser are organized alphabetically by sub-topic. The FAQ page contains a list of common questions and issues. If after consulting all of these documentation links you still have an unresolved question or issue running our software, you can post a new issue to get help.