Download jmol jar

Support and operating systems. Users : how to install Jmol application for local, standalone use. Installing and Enabling Java Proteopedia wiki.

Has step by step instructions for both Windows and Mac OS X, and for the 5 most popular web browsers. Increasing java memory for the applet. Web site administrators : How to install the application on a web server to be delivered using Java Web Start. How to configure a wiki so that it uses the Jmol applet.

Developers : compile the latest Jmol source code via subversion access. Navigation menu Personal tools Log in Request account. Namespaces Page Discussion. Views Read View source View history. Jmol links Website Sourceforge. This page was last edited on 14 August , at The Jmol Console is used to input commands.

In this menu, click on the button 'Console' which will open the Jmol Console. Because the Console and Display Windows will almost always be used in unison, arrange the windows so that they do not overlap and both fit comfortably on your screen. Most people prefer a larger Display Window. To move the windows, click and drag in the header space. Option 1: Open the folder that contains your PDB file. Note: you may have to arrange the Jmol window and folder window in such a way that you can see both at the same time in order to click and drag the PDB file.

Option 2: If you have Internet access and don't want to store PDB files on your computer, in the console, enter the command:. Depending on the PDB file, the structure may appear in one of several formats: Cartoon or Backbone Format: displays the secondary structure of the protein, with sheets in yellow, helices in magenta, and loops and turns in white. Ligands are displayed in ball and stick, and ions and water molecules are in spacefill. Ball and Stick: displays all atoms in the structure including ions and water molecules in ball and stick.

Atoms are colored in CPK gray carbon, blue nitrogen, red oxygen. Note that hydrogen atoms are typically not displayed in PDB files.

Click the button below to see what your Jmol Window might look like. This is a ball and stick rendering. To rotate the molecule within the X-Y axes on the computer screen, For PC users: place the mouse cursor in the Display Window, hold down the left mouse button, and move the mouse. For Mac users: place the mouse cursor in the Display Window, hold down the mouse button, and move the mouse. F or Mac users: place the mouse cursor in the Display window, hold the mouse button down along with CMD, and move the mouse.

If the mouse you are using has a center rolling wheel, you can also zoom in and out using this wheel. Introduction Physical models of proteins are powerful tools that can be used synergistically with computer visualization tools to explore protein structure and function. Welcome to the amazing world of proteins — and the fascinating stories that each one can tell! After download the download file and extracting it you should endup with a folder called "Jmol-x.

There are a number of files in the the folder, most of which are used to serve webpages containing Jmol applets. To run Jmol as a standalone application, the only file you need is "Jmol. For this tutorial, we will copy the "Jmol. Placing the structure files in the same folder as the "Jmol.