Once a structure has been determined, each atom in the structure is assigned an (X,Y,Z) coordinate to mark its location in 3-dimensional space. Molecular structures can be determined through the use of X-ray Crystallography, Nuclear Magnetic Resonance (NMR), or computer algorithm-based calculations. Drag and drop the shortcut to your desktop. In Windows, right click on the Jmol.jar file and select ‘create shortcut’. For convenience, it is a good idea to create a shortcut to this "jmol.jar" file on your desktop as well as in each of your working folders so you can easily launch Jmol. When first launching Jmol, you will need to click the "Jmol.jar" file (this will discussed in more detail in section 1-3). Jmol does not need to be "installed", so once these files are in place on your computer, the program will be ready to use. You may save this folder in any convenient location on your computer. Jmol File Location – The Jmol folder contains all the files your computer needs to run Jmol, and they need to be kept together in the same folder. Unzipping for Mac - If you are using a Mac that does not have an unzipping program, you may download the free unzipping software MacZip, available at: o If your computer does not have WinZip, you may download the free unzipping software CAM UnZip, available at: o Most computers running Microsoft Windows will automatically do this using the program WinZip. Unzipping Jmol - The program Jmol should download as one zipped folder that will need to be unzipped. For total functionality in designing a structure to be built on a 3-D printer, you must use the version 12.0.14 that is available on our website.ĭownloading Jmol - We suggest that you download jmol directly from the Center for BioMolecular Modeling's website to ensure you are using the correct version for creating physical models. 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. 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.
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