Include only the hetero group listed in the table.įinally, do not leave water molecules on display in any of your The table of assigned files, do not include them with any of the If there are hetero groups in addition to the one listed in ![]() If your protein contains two or more identicalĬhains, restrict all views to one chain and its associated hetero To test a script, type the following command at the prompt in the Rasmol Script console window:įor this to work properly, the Jmol.jar file, your pdb file and the script file should all be in the same folder.Īfter a delay of a few seconds, you should see the script you created. Use the "show orientation" command to create "moveto" command, and then include the "moveto" command in your script. Once you have constructed a described scene, use rotation, translation, and zooming to a produce clear, informative view in which the features requested are clearly displayed. When loaded into Jmol, each will recreate one of the scenes described below. You will create a collection of five script files. All your script files should be named xxxx#.spt, where xxxx denotes the four character PDB file ID for your protein, and # is a one-digit number (example: 1cyo2.spt). Your instructor will demonstrate how to make your script files with BBEdit and then load them into Jmol. Obtain your structure file from the Protein Data Bank. All the assigned proteins contain a hetero group, which comprises a cofactor, prosthetic group, or inhibitor. You will also write a brief description of the protein, its interaction with the hetero group, and some of its structural features.Įach of you will work with a different protein. ![]() Scripts are files that can be loaded into Jmol to execute a series of commands and regenerate a scene. You will prepare a series of scripts, test them, and submit them for evaluation. Each of you will be assigned a different protein. In this assignment you will explore the structure of a protein using Jmol. Chem406:Biophysical Chemistry Assignment For Lab 3-Jmol
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