Section I – Using Jmol as a Computer （节我u2014u2014使用Jmol电脑）.pdf

version 1.0 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. Section I of this Jmol Training Guide is designed to introduce you to this software. This program is a simple, yet powerful tool, which enables you to visualize a molecule in 3-dimensional space. As you actively manipulate the computer mouse to rotate the molecule, you will develop a sense of the 3-dimensional nature of a protein. Through the Jmol command line, you can also change the display format of the molecule to display different features of the molecule. 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. 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. Therefore, as you learn to generate different images of proteins in Jmol, you will also be designing a physical model of that protein. Welcome to the amazing world of proteins and the fascinating stories that each one can tell. At the end of this section, you should be familiar with how to use Jmol as a computer visualization tool. 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 Files