PyMol Problem Set 2010 - PyMol Problem Set Due in class on...

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PyMol Problem Set Due in class on February 9, 2010 This problem set has been designed with two goals in mind: it is meant to teach you some of the basic principles of protein structure and to introduce you to the use of PyMol for the analysis of biomolecules. While there are alternative (and sometimes even free!) modeling programs that can also be used for this purpose (e.g. Insight, Chimera, and SwissPDB Viewer), Pymol is easy to use, produces excellent graphics, works on ordinary PCs and Macs, and is free for you to download. It is available from the following site: You can also Google “PyMol” and follow the links to the free versions. The following instructions should work on either the Mac or the PC version. After installation of the program, download the following PDB files from the PyMol Problem Set Folder on the course web server: Human Myoglobin.pdb Horse Heart Myoglobin.pdb GFP.pdb Cytochrome bc1 monomer.pdb Cytochrome bc1 dimer.pdb 1K4C tetramer.pdb (several individual files) Start by loading one of the files and playing with the program for a while. Experiment with the mouse buttons to learn how to rotate structures and zoom in and out. At the bottom right, the program shows a rather cryptic list of commands that can be executed using the mouse in combination with various modifier buttons (like “shift”, “Control”, etc.). Note that the default command set is for a 3-button mouse. If you only have two buttons, choose “Mouse Two Button Viewing Mode” from the menu bar at the top of the program. The top pane of the interface is used to enter commands, and the bottom pane shows the molecular structure. At any time, you can type “help+<return>” to get a list of commands that you can use. You can also download the instructions from the web site. This program uses a rather complicated syntax for selecting residues or specifying a portion of the protein to work on, which is worth learning if you plan to use it a lot. For our current purposes, however, you will only need the commands described below. Also, as a helpful hint, if the molecular viewing pane fills up with text such that your structure disappears, you can get your molecule back by pressing “escape”. You may not need this information, but you will be glad I told you if it happens! The pane on the right side lists all of the files that you have open, along with abbreviated menus for changing the display. Click and hold a letter to pull up its submenu of options. The “A” button specifies “actions”, like removing atoms, deleting objects, or aligning sequences. The “S” button “shows” various aspects of a structure, such as the “sticks” of the amino acids, the ribbon “cartoon”, the space-filling “spheres”, and the solvent accessible “surface”. Note that more than one of these aspects can be on at any given time. The “H” button serves to “hide” the same aspects. You can select “H everything” to turn off all display modes. The “L” button shows
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PyMol Problem Set 2010 - PyMol Problem Set Due in class on...

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