Flight of the Flagellin

What is this page really? Well, we recently discovered how easy it is to import 3D protein structures into an open-source flight simulator called FlightGear. It seems pretty ridiculous, but this could be a great way of teaching protein or molecular structure to people both young and old. It's also really surreal to be bringing some of the smallest units of life, and exploring them, in the setting of some of the largest man-made vehicles.

Flying is just fun. Lots of people play flight simulators just to fly around some generated landscape. Now in this case, you're flying our somebody's hard earned scientific data instead. With the amount of work that went into getting this data, it's hard to say whether we're taking full advantage of it and using it to its full potential, or just completely bastardizing it.

Something like this could also lead into new games, like EteRNA or Fold-it, in which the player is assigned the puzzle of solving a protein or RNA structure. The higher your score, the better you did, and your solution can actually contribute to scientific data. More specifically, we can swap out that plane model for, say, a ligand. Then, using this same idea, we can power docking experiments, in which players have to try and land a ligand in the active site of an enzyme, for example. This kind of computer modelling is common practice in drug design.

The Game

Download and Installation:

First download and install the game from http://www.flightgear.org/

Next, download and install the Flight of the Flagellin Maps! We wish we could make this a little bit easier but, we're inexperienced! Follow these step by step instructions:

• Download and extract the map files: proteinflight.zip
• Install the map files:
  1. Edit Objects/w080n40/w072n42/1777947.stg with any simple text editor.
  2. Scroll to the bottom of the file.
  3. Replace YOURPATHHERE with the file path to your downloads folder, or wherever you choose to store the protein models.
  4. Copy the Objects and Terrain folder to your Flightgear Scenery folder, ex: c:\Program Files\FlightGear\data\Scenery.
• Run flightgear and pick to take off from the Boston Airport! (ID:KBOS)

Below are a series of challenges that we have made in our level:

Challenge #1: Flight of the Flagellin

In your glider, fly down through the helical constant domain of the flagellin monomer, landing safely in the Boston airport. (Right in time for the world finals :) ). Bonus: The larger the aircraft you can fly through, the better.

Starting Coordinates:
Latitude: 42.472766
Longitude: -71.028729
Altitude ASL: 27059.96
Heading: 166.5

Challenge #2: Red Fluorescent Protein

Land a helicopter on the chromophore of RFP. To make it easier, we've put a nice flat landing pad there for you.

Challenge #3: Land on beta sheet

Land any plane on the beta sheet. The larger the plane, the better. Need more of a challenge? Make the betasheet smaller.

Import your own proteins!

Here we'll talk a bit about how we actually did it. Basically,

1. Get the ePMY version of Blender or another 3D design software.
2. Import PDB files, increase the size, rotate and manipulate as needed. Save as .AC format See this link for the plugin.
3. Insert your objects into your favourite city using this guide.
4. Fly, fly away!