VMD User's Guide

new view, and enter resname SO4 CO to select the SO 4 ion and the CO molecule, and choose thedrawing method ‘VDW’ to render them as Van der Waal spheres. Once again, press the CreateRep button and enter resid 93 64 to select the two histidines, and render them as ‘CPK’. If youfollowed all that, then congratulations, you have made a nice image of myoglobin! With furtherexperimentation you should be well on your way to learning how to use VMD.2.3 Rendering an ImageFind an interesting view of the molecule from the previous tutorial. Suppose you want to publishthis view in a journal and want a high quality image, or you want to make a large poster. Taking theimage from a screen capture often results in a rather grainy image as the size of the pixels becomesapparent, so you want something with more resolution. There are several programs available whichcan render a high-quality raster image, based on an input script. VMD has the option to createinput scripts for many of these image processing programs, which may then be processed to createa higher quality image of the scene displayed by VMD at the time the script was created. SeeChapter 7 on rendering for a further description of how this works.Open the Render form [§ 4.4.11] and select ‘Tachyon’ from the Render Using menu. Both of thetext boxes will be filled with default values which should not need to be changed for the purposesof this tutorial. Press the Start Rendering button. After a few moments of processing, you souldsee the messageInfo) Rendering complete.in the VMD text console. If everything worked correctly, you will end up with an image filenamed plot.dat.tga (on MacOS X or Unix) or plot.dat.bmp (on Windows) in your current workingdirectory. This image is in either Windows BMP or Targa graphics format, and can be read bymany programs (such as display, ipaste, xv, Gimp or Photoshop).2.4 A Quick AnimationAnother strength of VMD lies in its ability to playback trajectories resulting from molecular dynamicssimulations. A sample trajectory, alanin.dcd is provided in the proteins directory includedwith VMD. To load it, open the molecule file browser as described previously. Next click on theBrowse button and select the alanin.psf file in the file browser. Once selected, press the Loadbutton to load the structure file. Next, select the alanin.dcd file and load it as well. This willread the DCD trajectory frames into the same molecule with the previously loaded alanin.psffile.In the display window you should see a simulation of an alanin residue in vacuo. It isn’tparticularly informative, but you can easily see that the structure is quite unstable in an isolatedenvironment. After the DCD file has loaded, animation will stop. To see it again or to fine- tuneplayback, use the animation controls [§4.4.3] found at the bottom of the main VMD form. Pressthe button that looks like > to play the animation. Use the Speed slider at the bottom of the formto change the speed of playback. By rotating the molecule around, etc. you should get an ideaabout how the system destabilizes over the course of the simulation. The animation controls aregenerally similar to what you’d find on a DVD or CD player.16