![]() ![]() ![]() ![]() If you have placed the 1liu.pdb in this folder, you should see it, if not, you will need to navigate to its location. An open dialogue window should appear showing you the files that are located in the same folder as the Jmol.jar file. After the application window opens, select Menu bar:File:Open. Launch Jmol by double-clicking on the icon for the Jmol.jar application file. Launch Jmol and open the 1liu.pdb structure file. Regardless, the upside of this method for interacting with Jmol far outweigh the downsides. Those of you who have used computer operating systems for longer than a decade (two decades in the case of Macs), such as Unix or MS-DOS, know what this is like. There is a downside to this approach, however you need to know what commands to type before you can type them. For this reason, we are going to skip the first two methods and go straight to this one. This method offers complete access to Jmol's commands.Using the Rasmol Script console window to enter commands in a command line. ![]() This method offers more options than the first but it is still lacking, particularly with options for selecting atoms.Using the popup menus that appear when you in the application window.There are so few commands available using this method that it is essentially useless.Using the menus in the Jmol application window.In the Introduction we discussed that there are three ways to enter commands with the standalone version of Jmol: With Jmol model building is a two step process: you first select the that atoms you wish to work with and then tell Jmol what you want to do with the atoms you have selected. Building models with Jmol works a little differently than snapping balls and sticks together. While looking at some of the models that we will be creating with Jmol, imagine building these with the ball and stick model kits that you have used to build models of small molecules. One of the huge advantages of using computers to create molecular models is the speed at which they can convert a list of atomic coordinates into a three-dimensional model. ![]()
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