All or part of a protein structure (for example) may be compared. RMSD below 2.00 A is generally considered an excellent fit or match. The lower the RMSD (usually expressed in angstroms), the more alike the two structures are. In order to calculate an RMSD, two (or more) structures must be compared, and one is referred to as the reference structure. It actually refers to the RMSD of the positions. RMSD stands for root-mean-squared deviation. We will investigate a few plugins now, and use many more of them later on. The default set is pretty good, but this can be fun to play with.įigure 4: Light 0 has been moved behind the molecule! With this selection, under “ Mouse.Move Light ”, you can reposition the virtual lights which illuminate your render. Note that there is currently no way to undo Move operations, so the atom coordinates should first be saved to a file.

After you click “ Save ”, you are prompted for a directory and file name.īe careful! The VMD User’s Guide has this warning:

You must make sure you choose “ all ” in the “ Selected Atoms ” pull-down, and “ PDB ” in the “ File type: ” pull down. So, what if you want to save these changed coordinates? At this point, the easiest thing to do is choose the “ File.Save Coordinates ” main menu selection. This only changes the coordinates on screen, however, unless you save the new coordinates through the menu or tkconsole.įigure 2: Result of using “move.Residue” (shortcut 6). With “move”, you can actually change the coordinates of atoms, fragments, residues, molecules, or representations (recall that each of these definitions are different!). The move command can be activated through the menu as above, or by typing the appropriate number (5, 6, 7, 8) in the main viewer window while it is active. You can temporarily hide the label by clicking the “ Hide ” button. To delete the labels on-screen, simply highlight the label (remember to pull down the proper label type on the left-hand top of the “ Labels ” menu!), and click “ Delete ”. This is important to remember when you have cluttered your display with many labels, lines and angle markers and you need to get rid of them all.įigure 1: Illustrating the different VMD labels: labels (green) bonds (white) angles (yellow) and dihedrals (blue). (You will see later that VMD doesn’t really know if atoms are bonded unless we give it addtional information, anyway).Īside from displaying actual labels on the screen, it makes a list of the labels under the “ Graphics.Labels ” menu, which pops up a floating window. Actually, “ bond length ” really means “distance between two atoms” as the atoms do not need to be bonded. However, label includes structural information such as bond length and angular information. At first glance, label seems to be like query, except it puts a label on the display. ”, or by typing 1, 2, 3, or 4 (for atom, bond, angle or dihedral) in the viewer window when it is active. The label commands can be activated by selecting “ Mouse.Label. The information shows up in the terminal window that VMD produces when you start the program. If you click on an atom, and it appears nothing happens, don’t worry. To enter query mode, type “0” (that’s a zero) in the display window, or select “Mouse.Query” from the main VMD menu. The query command gives information about the atom clicked on. Mostly found under the “ Mouse ” main menu item. It is relatively simply to learn a bit of TCL or python programming in order to script some repetative task that you might have to do in VMD.Įxplore the basic tools of VMD, including some plugins, and learn basic scripting syntax in order to extend the functionality of VMD. A list of these scripts may be found here. In order to uses plugins, you normally have to use the tkconsole, load the file, and then issue commands to extract the functionality. Plugins are usually script files, written in TCL or python (programming languages). We will focus on the “Analysis” type of plugins during this session. Many plugins find their way into the default VMD distribution eventually. A list of such plugins may be found here. Plugins are menu items that researchers have added into VMD in order to extend the basic functionality. Aside from the very basic tools (picking and measuring tools, for example), there are also a large number of plugins and scripts. There are many useful tools in VMD which allow us to extract useful information.

Vmd atom selection coordinates