Visual inspection of the PDB file reveals that the chain D is the ligand. It looks pretty complex, so let's simplify the view by displaying parts that are important for your assignment. That the active site contains a catalytic triad, consisting of Ser, His, and Asp residuesĪ suitable structure of chymotrypsin with a bound inhibitor in the PDB file 1AFQ.That the active site has a pocket that accommodates an aromatic amino acid residue from the ligand.That a ligand (the substrate or inhibitor) is bound to the active site.Your second homework assignment asked you to create an image that illustrates the following aspects of the chymotrypsin mechanism:
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For effective use, you should download and use it from your personal computer. This program is available for many computer platforms, but it runs slow on our SGI workstations. The commands are explained in the PyMOL manual. This is the most powerful way to interact with the program, but requires that you are familiar with the logic and syntax of PyMOL commands. For example, you can create dashed lines (a good way to show hydrogen bonds) between oxygens and nearby amide hydrogens in the alpha-helix by using a command "dist (helix and name o), (helix and (name h and neighbor name n)), 2.5". The command line allows you to type in commands that can accomplish almost any of PyMOL's functions.For example, you can select two atoms (first by CTRL-SHIFT/left-clicking, second by CTRL-SHIFT/right-clicking ) and create a covalent by pressing CTRL-T. Furthermore, you can select and perform specific tasks via mouse and keyboard shortcuts. Your three-button mouse allows you to rotate, move, and zoom in/out by holding down the left, middle, or right button, respectively. The molecular display area allows one to view and interactively manipulate molecules.For example, you can show your protein as a gray surface and the inhibitor as green sticks if you have separated them into two different objects. A task bar on the right side of the screen allows one to select which objects are displayed in which way.For example, you can change the display quality settings, the background color, the size of your spheres, or the transparency of the surface from the pull-down menus. Pull-down menus provide access to the file functions, the molecular editor, the program options, and a few more advanced tasks.You can interact with the program via four complimentary ways As a result, it takes a little time to learn the program. During the early development, emphasis was placed on functionality, and not on intuitive user interface. At the present time the program is still undergoing active development, but it is mature enough to be used for learning and research.
Two unique and valuable features of this program over some other visualization program are the use of the powerful programming language ( Python) and an emphasis on high-quality graphics. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research. Warren DeLano, PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The nucleophilic alkoxide anion then attacks the carbonyl carbon in the peptide bond.Īccording to the program's author, Dr. These three residues form a hydrogen-bonding network that allows deprotonation of Ser195 during the reaction.
PyMOL Tutorial: Chymotrypsin Chem 110L: Macromolecular Visualization Laboratory Exercise: PyMOLĬhymotrypsin is a well-studied proteolytic enzyme that functions in our digestive tract where it assists in the hydrolysis of proteins that we eat.
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