About this tutorial...

1.- Goals

2.- Tutorial Structure

3.- How does it technically work?

Four interacting components integrate the whole e-learning application
  1. The Protein Data Bank (PDB). It is a repository for 3-D structural data of biomolecules, typically determined by X-ray crystallography or NMR spectroscopy. Data is submitted from laboratories around the world and can be accessed for free at http://www.rcsb.org  The biomolecules studied in this tutorial are obtained from this repository. More about the PDB.
  2. PyMOL is an open-source molecular visualization program. It is well suited to producing high quality images of small molecules and biomolecules. http://pymol.sourceforge.net/ More about PyMOL.      
  3. Mozilla Firefox is a free web browser. You should be reading this text in it. Other web browsers might also work for this tutorial, but they have not been tested. http://www.mozilla-europe.org/
  4. The PyMOL handler is a small application developed at the Molecular Bioinformatics Laboratory - J.W. Goethe University Frankfurt. It establishes the communication between the web browser and PyMOL and is key for this tutorial.

The following scheme illustrates how the 4 components interact with each other. The user will follow the tutorial at the Firefox window (right). Clicking on links has an effect on the PyMOL window (left), which is achieved by connecting Firefox and PyMOL through the handler (see below). If a biomolecular structure is needed, PyMOL will download it from the PDB.

4.- Installation of the required components

In order to pass commands to PyMOL from the web browser, a client program is needed. In addition your browser (note that only FIREFOX is supported) has to be configured to handle files with the extension .pymolrpc with that client.

In the following steps, the installation procedure of the required components is explained. Each step is illustrated with what you should be seeing in your computer as you proceed with the installation.

Step 1. Install Mozilla Firefox

For that go to http://www.mozilla-europe.org and download the latest version. Then double click the Firefox Setup.exe installer to start the installation.

Step 2. Install PyMOL

Follow the instructions from http://delsci.com/rel/099/#Windows

Step 3. Install the PyMOL handler

Download the client from here. After clicking, a window dialog similar to the one on the right will pop up. Choose "Save to Disk". Once the download is completed, unzip the file.
After unzipping you will see the contents of the folder. These are the files shown on the right. The program (which is the PyMOL handler) we need in a minute is called runpymol.exe. For everything to work properly, the config.ini file might need editing to point to the PyMOL executable. Open it with the Windows notepad, and you will see something like the following picture.

Edit that line, if it is not correct, so that it is specifying where PyMOL is installed in your computer.

NOTE that in a standard installation of PyMOL, on a Windows system in German, you will find that PyMOL is installed under: C:\Programme\DeLano Scientific\PyMOL\PyMOLWin.exe

Step 4. Associate the PyMOL handler with files with "pymolrpc" extensions

For the final step, we will launch PyMOL just from here. Click here to launch it!.

After clicking the link to "launch PyMOL", Firefox will ask (see right!) what to do with a file called "something.pymolrpc"

Choose "Open with" and browse your file system to find the runpymol.exe you just downloaded and unzipped. (See the figures below)

In order to automate future actions, mark the option "Do this automatically for files like this from now on", as shown in the following figure.

PyMOL will be automatically started, if you just clicked the "launch PyMOL" link. Wait until PyMOL completely starts and you see a message like the one shown in the figure below. Once you observe that PyMOL is running, click OK and the program will try to establish a connection.

Wait until the word "Ready" appears on the screen. From this point everything will run smoothly.

Have a lot of fun !!!

This tutorial has been developed at the Molecular Bioinformatics Laboratory - J.W.Goethe University - Frankfurt am Main
Send your questions and comments to: dgruiz AT bioinformatik DOT uni-frankfurt DOT de