Using PyMol

PyMol comes in two flavors, open source and commercial. Compiling on a linux-related platform should not be a problem, especially if you have the root privileges. If you do not, check what your IT guy has been up to. Also, if you are affiliated with a larger scientific institution, you may check whether the institutional license is available.

Any file with the extension "pml” should open in PyMol by doubleclicking. If the double clicking does not work, try opening PyMol first, and then searching for the *.pml file from the ‘File->Run Script ...’ drop-down menu.

To inspect the protein structure, you can press the left button and drag the mouse to rotate, right button and drag to zoom, and middle button and drag to pan. The S button in the lower right corner of PyMol opens the protein sequence on the top of the window. You can click on any residue in the sequence and little pinkish dots will highlight the sidechain on the structural model.

Good starting points for a PyMOl novice: Practical Pymol for Beginners or MacPyMOL_tutorial.