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VMD: a graphical tool for the modern chemists

2000; Wiley; Volume: 22; Issue: 1 Linguagem: Inglês

10.1002/1096-987x(20010115)22

1096-987X

Matthias Prall,

Distributed and Parallel Computing Systems

Visual Molecular Dynamics (VMD) is a molecular graphics program distributed by the University of Illinois at Urbana–Champaign, and designed for the interactive visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, and membranes. It is available for SGI workstations with IRIX 5.3 or higher, Hewlett-Packard workstations with HP-UX 10.20, Sun workstations with Solaris 2.6 or higher, IBM RS/6000 workstations with AIX 4.2 or higher, PCs running Windows 95/98/NT, or Linux. At its heart, this program is a general application for displaying molecules containing any number of atoms. It can read PDB files or use Babel (if available) to convert other formats automatically. Once loaded, user-defined subsets of the molecule can be displayed in various ways including simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes, ribbons, van der Waal spheres, and molecular surfaces. The display can be saved directly to a postscript file or in a format suitable for use by ray-tracing programs such as Raster3D, POV, and Rayshade. VMD can read molecular trajectories from DCD and Amber files, or it can acquire time steps from a running molecular dynamics program. The data can be used to animate the molecule or to plot the change in molecular properties such as interatomic distances, angles, or dihedrals over time. VMD can be used as a graphical front end to a molecular dynamics (MD) program running on a remote supercomputer or high-performance workstation. VMD can interactively display and control the MD simulation as the simulation is running. The user can disconnect from the simulation and let it continue, reattach to a running simulation, or halt the MD program. A number of different visual display and control systems are supported in addition to the usual monitor, keyboard, and mouse. The UNC tracker library is used to get position and orientation information from a wide variety of spatial input devices, including a Polhemus Fastrak. An interface to the CAVE library has been developed for use in many different types of stereoprojection facilities. VMD uses the freely available Tcl scripting language for processing text commands. Further information about VMD is available from www.ks.uiuc.edu/Research/vmd/. This report refers to the Windows NT and the Linux 1.4 versions. VMD starts up in a text console, a display window entitled "VMD OpenGL," and a button bar entitled "Main." Text commands are typed in the console window, graphics are displayed and manipulated in the display window, and many commands are available from the menu interface, accessible through the button bar. There are two ways to perform almost all functions in VMD—either use the menu buttons or the text console. For many of the commands, a pop-up menu is available in the display window by pressing the right mouse button (on a mouse with three buttons). Some of the more sophisticated commands, such as Tcl scripting, are only available in the text interface. The layout of the windows and menus in the NT version is somewhat different from other Windows programs, but after a while it is easy to use. The molecule specifications (easily available via the Internet) are loaded from the Mol menue. For the test purposes, a PDB (Protein Data Bank) containing the atomic coordinates for a calicheamicin γ1′–DNA complex (Kumar, R. A.; Ikemoto, N.; Patel, D. J. J Mol Biol 1997, 265, 187) was used (Fig. 1). A disadvantage may be that the NT version is not able to handle more than one hard drive partition, namely the partition where VMD is installed. A screenshot from VMD displaying a calicheamicin γ1′–DNA complex. The mouse is used to manipulate the structure in the display window in the three basic mouse modes—rotation, translation, and scaling. The mode can be changed from the display window pop-up menu by pressing the right mouse button and picking the option under "Mouse Mode" or by pressing r, t, or s on the keyboard. Unfortunately, the pop-up menu only works with a mouse having three mouse buttons. As many Windows pointer devices only posess two buttons, the menu is not available in this case. By default, the bonds are represented as lines, and nonbonded atoms as points, with the color in both cases representing the atom type. As mentioned above, many different drawing modes are available from the "Graphics" menu. Together with the "Atom Selection" keyword line in the same menu, this is a poweful tool to generate outstanding representations for biochemical molecules. As shown in Figure 1, it is possible to represent, for example, the protein backbone in the "Ribbons" mode, the nuclear bases as "CPK" models, and the enediyne moiety as "Licorice" in an easy way. The "Coloring Method" chooser allows coloring of different atoms, atom groups, chains, segments, and residues. The VMD "Atom Selection" method is very helpful when generating attractive, informative, and complex graphics. Atoms may be selected on the basis of a property, i.e., protein or not, water, or nucleic backbone. They may also be selected by atom name, by residue name, or by many other identifiers. VMD can handle regular expressions, so that name "C.*" will select all atoms with names starting with C. The boolean operators and, or, and not, can also be used, so the selection all and not name "N.*" selects all nonnitrogen atoms in a protein. Several more abstract selection criteria are available. For instance, the selection mass>12 and mass<14 selects all atoms with mass greater than 12 and less than 14 atomic mass units. Many math functions are also provided, so the selection sqrt(sqr(x) + sqr(y) + sqr(z)) < 10 will select atoms in a spherical region of radius 10 centered about the origin of the coordinate space. VMD has the option to create input scripts for many image processing programs, which may then be used to create a higher quality image of the scene displayed. This does not work very well for the POV Ray input in the Windows version, as the rendered image is not the same as the one displayed in the VMD graphics window. A further deficiency is the lack of creating raster image files like GIF, TIFF, or JPG. In the Linux version, the SGI image format RGB is available, which then can be transformed into the appropriate format by image viewers like xv. The standard windows graphics software is not able to read RGB files. It is also possible to generate PostScript files, but they have a poor resolution and have not very much in common with the beautiful on-screen representation. Direct printing of the screen is quite difficult in the Linux version, where the command has to be typed in a command box. Direct printing is not possible in the Windows version. Another application of VMD lies in its ability to play back trajectories resulting from molecular dynamics simulations. By loading the appropriate DCD file, the display window shows a simulation of the motion of the chosen system. In the "Animate" menu, the speed or style of the playback can be adjusted. The "Display" menu controls many of the characteristics of the graphics display window. The characteristics that may be modified include "Depthcue," "Axes," "Detail," "Perspective," "Stereo," and "Lights." The last two items are the most interesting. With the "Stereo" drawer, different 3D display modes are accessible that make it possible to see the structure three dimensionally (e.g., by crossing the eyes). With the "Lights" chooser, four different light sources are available that illuminate the molecule from different angles and with different intensities. Additionally, the clipping planes can be varied so that slices of the molecule can be displayed. An advanced tool that is worth mentioning is the ability to customize the menus. New submenus and items can be added to the pop-up menu, and text commands can be assigned to those items. When the items are selected by the user, the assigned text command will be executed as if it had been typed in at the console. In fact, with Tcl, arbitrarily complex commands (such as scripts) can be assigned to a single menu selection. VMD is a great tool for displaying and modifying chemical structures. It easily reads different input files and displays the molecules in many modes. With the interplay between different drawing, selection, and coloring methods it is possible to generate outstanding and clearly arranged representations of bioorganic molecules. Nevertheless, there are a few bugs that have to be removed. As the Linux version works nearly perfect, the Windows NT version has to be improved, as many menus, including the Help and the SIM menu, do not work. Additionally, the pull-down menu should also work with a two-button mouse, and many of the hotkeys should be fixed. Last, but not least, in both versions the graphical output as GIF or JPG should be added, and it would be nice if the POV Ray input produced the same image as displayed in the VMD graphical window. Hence, future improvements should also aim at the Windows users. In summary, VMD is a highly useful graphical interface for chemists and biochemists.