You should have downloaded a simple script, beta.tcl, with this unit. Just use any text editor to write your script file, and in a VMD session, use the command source filename to execute the file. When performing a task that requires many lines of commands, instead of typing each line in the Tk Console window, it is usually more convenient to write all the lines into a script file and load it into VMD. Thus, $crystal is now a function that performs actions on the contents of the “all” selection. This concept is particularly important when multiple molecules are loaded at the same time (see Basic Protocol 9 for dealing with multiple molecules in VMD). A top molecule means that it is the target for scripting commands. Instead of a molecule ID (which is a number), we have used the shortcut “top” to refer to the top molecule. This step creates a selection, crystal, that contains all the atoms in the molecule and assigns it to the variable crystal. The selection returned by atomselect is itself a command you will learn to use. The first argument to atomselect is the molecule ID (shown to the very left of the VMD Main window), the second argument is a textual atom selection like what you have been using to describe graphical representations in Basic Protocol 1. This command allows you to select a specific part of a molecule.

Type set crystal in the Tk Console window. If you are using a Mac, your vmd console window is the terminal window that shows up when you open VMD.Ģ. The Tcl commands that you enter in the VMD TkConsole window can also be entered in the vmd console window. It should tell you a molecule has been loaded, as well as some of its basic properties like number of atoms, bonds, residues and etc. The vmd console window tells you what’s going on within the VMD session that you are working on.

When you open VMD, by default a vmd console window appears. You can use the standard Unix commands in the VMD TkConsole window to navigate to the correct directory. If you see the error message ”Unable to load file ‘1ubq.pdb’ using file type ‘pdb’”, you might not be in the correct directory that contains the file 1ubq.pdb. In the VMD TkConsole window, type the command mol new 1ubq.pdb and hit enter.Īs you can see, this command performs the same function as described at the beginning of Basic Protocol 1, namely, loading a new molecule with file name 1ubq.pdb.

Animate secondary structure vmd