VMD User's Guide
VMD User's Guide
VMD User's Guide
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will load the corresponding structure and coordinate files into the same molecule. On the Windowsplatform, one must preface the <strong>VMD</strong> invocation with the Windows start commandstart vmd molecule.pdb• -h | --help : Print a summary a command-line options to the console.• -e filename : After initialization, execute the text commands in filename, and then resumenormal operation.• -python : After initialization, switch to the Python interpreter before executing commandsin the file specified by -e (if any), and leave the text interpreter in Python mode.• filename : Load the specified file at startup. The file type will be determined from thefilename extension; if there is no filename extension, and the filename contains 4 letters, it isassumed to be a PDB accession code and will be loaded accordingly; otherwise the format isassumed to be PDB.• - filename : Load the specified file using the given filetype.• -f : Load all subsequent files into the same molecule. This is the default. A new moleculeis created for each invocation of -f; thus,vmd -f 1.pdb 2.pdb -f 3.pdb loads 1.pdb and2.pdb into the same molecule and 3.pdb into a different molecule.• -m : Load all subsequent files into separate molecules. The -f and -m options may be specifiedmultiple times on the command line in order to load multiple molecule containing one or morefiles.• -dispdev < win | text | cave | caveforms | none > : Specify the type of graphicaldisplay to use. The possible display devices include:– win: a standard graphics display window.– text: do not provide any graphics display window.– cave: use the CAVE virtual environment for display, forms are disabled.– caveforms: use the CAVE virtual environment for display and with forms enabled. Thisis useful with -display machine:0 for remote display of the forms when the CAVE usesthe local screen.– none: sameastext.It is possible to use <strong>VMD</strong> as a filter to convert coordinate files into rendered images, by usingthe -dispdev text and -e options.• -dist z : Specify the distance to the <strong>VMD</strong> image plane.• -height y : Specify the height of the <strong>VMD</strong> image plane.• -pos x y : Specify the position for the graphics display window. The position (x,y) is thenumber of pixels from the lower-left corner of the display to the lower-left corner of thegraphics window.• -size x y : Specify the size for the graphics display window, in pixels.172