More in 3D

If you enjoyed studying the 3D structures of proteins in the "in practice" section, you can continue here. We have selected a few interesting proteins structures. There are many more structures available from the PDB.

Let's start with a few tips for using Yasara:

• View the help movies to answer your questions: Help > Play help movie
• Read the write-up if you still have problems: Help > Show documentation
• Hanka Venselaar has put together a short introduction to Yasara for additional support
• It doesn't hurt to try: if you mess up the settings, you can easily (re-)install the program
• Be patient: Yasara's performance depends on the power of your computer and the size of the molecule you are viewing.
• Be even more patient when making pictures: ray tracing is hard work, even for fast computers

Making nice pictures

When you write papers, reports, or essays you must support the content with clear illustrations. In other words: people like to see nice pictures. Making such pictures (and with some practice even nicer ones) in Yasara is very simple:

• Manipulate your protein to give a good overview of what you want to show. You may need to add labels for clarity.
• Then click File > Save As > Ray-traced screenshot
• Tweak the settings and choose Run PovRay and save bitmap
• Select a sensible file name and adjust X and Y
• Note: the aspect ratio of X and Y must be equal to the one of the Yasara screen. For example: 4:3 if you use a screen resolution of 1600x1200
• When you click OK, it is just a matter of time before you have your picture.

Interesting proteins

Here is a list of interesting protein structure files. You can view them all by opening them in Yasara: File > Load > PDB file

• haemoglobin.pdb contains the quaternary structure of the oxygen transport protein haemoglobin. If you have this specific form of the protein in your blood, your health is very poor. Can you figure out why? Hint: look at the molecules bound to the four haem groups.
• dna.pdb contains a short DNA-helix. The bases pair are not entirely correct. There are also many zinc ions in the structure. Do you know why? Hint: think about charges.
• chaperonin.pdb contains a very impressive protein complex: GroEL/GroES. This is a so-called chaperonin. It forms a cage around an unfolded protein to protect it from unwanted interactions with other proteins while it folds.  Note: you should skip this structure if you have a slow computer.
• rubisco.pdb contains the most abundant protein on the planet: rubisco. It is involved in photosynthesis.
• aquaporin.pdb contains a water channel that can be found in many cell membranes. If you look well, you can see the channel between the helices.
• potassium.pdb contains a potassium channel. This type of channels is very important in the signaling process of the nerves. However, this particular channel is found in a bacterium.
• plaque.pdb contain a so-called amyloid plaque. That is a tall stack of improperly folded proteins. Plaques like this one cause afflictions like BSE, Alzheimer's disease, and Huntington's disease.