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Tutorial 2 - Using the GUI

This information is to help users become more comfortable with the GUI interface for the rDock platform. It will not provide information on how to use the rDock command-line interface.

Using this tutorial

To use this tutorial you should make sure that rDock is installed and first follow the instructions in the installation guide to install and set up the graphical user interface (GUI) - the installation guide is available on the same page as the GUI (ancillary programs). Also download gui_tutorial.zip, which contains all the files you need to run this tutorial; it is also located on the tutorial page.

Installing and running the GUI

Required other programs

You must have rDock installed and the appropriate path variables set up forit (see the rDock documentation).
You must also have java installed on your machine so you can actually run the GUI.
Babel should also be installed and the path set up for it, this is only necessary if you are going to use the GUI to convert pdb files - you can also create a mol2 file by saving a pdb as mol2 in DSVisualizer.
To use the view functionality DSVisualizer should be installed.

Installing the GUI

Unzip or untar the folder called rdock_gui.zip or rdock_gui.tar. This should give you an outer folder called rdock_gui with an inner folder called gui. In the outer folder you'll find a template file called path_template.txt which contains two lines, one starting GUI: and the other starting Protocols:.

After GUI: you should type the full path of where the script Completeeerrors.pyc, and rdock2.jpg, these should at the moment be in the same folder as the template that your editing but they don't have to be as long as they are all in the same folder and path_template.txt doesn't get moved as well.

After Protocols: you should type the full path of where all your docking protocols are, they should be in their own folder that has no sub folders(the default location is 2006.2_release_FC3/data/scripts/). Please save this folder and don't move it from this location – you can move the other documents in this directory – as long as you change it in the template, but you cant move the subdirectory gui. All paths should have no spaces in them.

After you edit path_template.txt :

$cd rdock_gui/gui/
$make all
$make doc
$make compile
$javac *.java

After you execute these commands you can run the gui from every location by typing:

$rDock_gui

or simply:

$cd rdock_gui/
$java gui.Main_gui

To uninstall it:

$cd rdock_gui/gui/
$make clean