VMD User's Guide

Main form4.4.1 and choosing the Load Data Into Molecule. . . menu item. Once the form appears,select the file you want by using the file browser or by typing the filename into the text entryarea. By default VMD will try to guess the type of file you are loading by matching the filenameextension with one of the file reader plugins in the file type list (the available file types are describedin Chapter 3). If VMD is unable to guess the appropriate file type or guesses incorrectly, you mustselect it from the list manually.You can control into which VMD molecule you want to load your data by selecting it fromthe Load files for: popup menu at the top of the form. If the file being loaded is intended for anew molecule, select New Molecule instead. If the file being loaded contains additional coordinateframes, electron density map, or other ancillary data for an existing molecule, choose the appropriatemolecule from the selection list at the top of the form. If the file being loaded contains trajectoryframes , you have the option of loading a subset of the trajectory skipping ranges or strides of framesrather than the whole thing. You can also select for VMD to load all frames before continuing on,or to load them in the background so that you may continue to interact with the menus and formswhile it loads additional frames . If the file being loaded contains multiple volumetric data, youmay select which data sets you would like to load.Once you have selected the file to be loaded, the appropriate file type, and the way it will beloaded, press the Load button and VMD will being loading the selected file. Any informationalmessages, errors or warnings which occur while loading the file will appear in the text window.Reading Trajectory FramesVMD can read in new coordinate sets from one of several file formats such as PDB, CRD, DCD,or Gromacs files. The new coordinate sets are appended to the end of the stored frames for theselected molecule. Loading coordinate data is like loading any other file, select it with the filebrowser make sure the file type is set correctly for the file being loaded, and then press the Loadbutton.By default, VMD will load all of the frames contained in a coordinate or trajectory file.Sometimes you may not want to read in a whole coordinate or trajectory file. For example, youmay only want the last frame, or every tenth frame. You can do this by changing the options in theFrames control of Files form. The Frames controls consist of three numeric input fields labeledFirst, Last, andStride. These make it possible to use a subset of the frames, starting at frame Firstand selecting every Stride frames until the Last is reached. For instance, to select every fifth framebetween frames 14 and 98, set:• First to 14• Last to 98• Stride to 5(Remember that frame numbers in VMD start at 0, so frame 0 is the first frame.) The value‘-1’ is a special number; setting First to -1 is the same as starting at the first frame, Last =-1isthe same as ending at the last frame, and Stride = -1 is the same as taking one step.4.4.5 Mouse MenuThe Mouse menu indicates and controls the behavior of the mouse when the mouse moves andclicks within the graphics window. Mouse clicks and drags can affect VMD in one of two ways. It34