Because Jmol is freeware and an open source program, it can be obtained from many locations. We will introduce you to the basic features of Jmol, including: Section 1: Using Jmol as a Computer Visualization Tool 1-1 - Downloading Jmol 1-2 - Protein Data Bank (PDB) Files 1-3 - Launching Jmol and Opening a PDB File 1-4 - The Command Line and common Display Formats and Display Colors 1-5 - The Select Command 1-6 - Boolean Operators 1-7 - Exporting Images 1-8 - Saving Your Work and Organizing FilesĪbout Jmol – Jmol runs on a Java platform and therefore functions equally well in a PC or Mac environment. Welcome to the amazing world of proteins - and the fascinating stories that each one can tell.Īt the end of this section, you should be familiar with how to use Jmol as a computer visualization tool. Therefore, as you learn to generate different images of proteins in Jmol, you will also be designing a physical model of that protein. Recent advances in 3-D printing technology makes it possible to generate a physical model of any virtual image of a protein generated in the computer environment of Jmol. At the MSOE Center for BioMolecular Modeling, we believe that physical models of proteins are powerful tools that can be used synergistically with computer visualization tools to explore protein structure and function. Through the Jmol command line, you can also change the display format of the molecule to display different features of the molecule. As you actively manipulate the computer mouse to rotate the molecule, you will develop a sense of the 3-dimensional nature of a protein. This program is a simple, yet powerful tool, which enables you to visualize a molecule in 3-dimensional space. Section I of this Jmol Training Guide is designed to introduce you to this software. Use the reference as a means to an end, not as the end in itself.Section I – Using Jmol as a Computer Visualization Tool Jmol is a free open source molecular visualization program used by students, teachers, professors, and scientists to explore protein structures. Keep in mind that you should have a vision of what you want to accomplish before consulting a scripting reference. Olaf University is an exhaustive list of Jmol commands. The Interactive Script Documentation from St. There are many more Jmol commands than the ones covered here. subset strucno=19 select all cartoon on color orange.select all cartoon off wireframe off spacefill off.Type or copy the commands below into the console. Let's select, subset, and display a single alpha helix. The select strucno=X command will select entire secondary structural elements, such as α-helices and β-sheets. To see a list of structural elements to which selected atoms belong, type the show structure command in the Console after selecting some atoms. select resno=36 wireframe 70 spacefill 100 color cpk color cartoon red (display residue 36 on both chains A and B)Īnd see if you can spot the revealed amino acid residues! Many PDB files contain additional information about the secondary structures present in proteins.Logic operators can also be used to chain together resno selectors, or in combination with other kinds of selectors. Again, hovering over any atom in an amino acid will reveal its position in the amino acid sequence. This can be done using the select resno=X command. When dealing with proteins, selecting specific amino acid residues is often desirable. To determine atom numbers, click on the Jmol window and hover over the atom of interest. select atomno=X or atomno=Y, for instance, selects atoms X and Y. Set-logic operators like and, or, and not can be used to specify multiple atoms. To select a few atoms, use select atomno=X. Think about what kind of object you'd like to select when deciding on what selector to use. Selecting an atom or group of atoms is almost always the first step in entering Jmol commands. select (chain=B) color lightgreen (color chain A light green).select (chain=A) color lightblue (color chain A light blue).select protein cartoon only (turn on "cartoon" display mode).hide waters (hide water molecules in the structure).Either copy and paste or type the following commands into the Console: Open the Jmol Console by typing console on in the command box below the window. Applying a set of basic commands illustrates the secondary structure of the protein well. Now, try entering some commands on your own! The Jmol window at right shows the structure of an HIV reverse transcriptase.
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