README file for VMD 1.8.3 --------------------------------------------------------------------------- What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/ --------------------------------------------------------------------- VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecule. VMD can be used to animate and analyze the trajectory of molecular dynamics (MD) simulations, and can interactively manipulate molecules being simulated on remote computers (Interactive MD). VMD has many features, which include: o No limit on the number of molecules, atoms, residues or number of animation frames, except available memory. o Many molecular rendering and coloring methods. o Extensive atom selection language with boolean and algebraic operators, regular expressions, distance based seelections, and more. o Extensive graphical and text interfaces to Tcl, Tk, and Python to provide powerful scripting and analysis capabilities. o Stereoscopic display with shutter glasses, autostereoscopic flat panels, anaglyph stereo glasses, and side-by-side stereo viewing. o 3-D interactive control through the use of joysticks, Spaceballs, haptic devices and other advanced input devices, with support for Virtual Reality Peripheral Network (VRPN). o An extensible plugin-based file loading system with support for popular formats such as AMBER, CHARMM, Gromacs, NAMD, PDB, X-PLOR, and others. Automatic conversion is supported through the use of Babel. o Export displayed scene to many popular file formats including POV-Ray, Raster3D, Renderman, Tachyon, and STL or VRML2 files for 3-D printing. o Perform interactive molecular dynamics (IMD) simulations using NAMD, Protomol, or other programs as simulation back-ends. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD. See the NAMD page for details: http://www.ks.uiuc.edu/Research/namd o Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that collaborators can work together over the internet. See the BioCoRE page for details: http://www.ks.uiuc.edu/Research/biocore What's new in VMD 1.8.3? ------------------------ User Documentation Updates o Source code documentation is provided online and is updated nightly. User Interface Changes o New controls and text commands for changing label text size o The defalt behavior of the isosurface representation slider is to calculate an isosurface with half as many samples per axis while the slider is being dragged, providing a much faster interactive rendering rate, followed by a full resolution isosurface computation when the slider is released. In cases where it is desirable to get a full resolution isosurface as it is being adjusted, holding down any of the shift/ctrl/alt keys will force VMD to calculate the isosurface at full resolution even while dragging the slider. o Isosurface reps are automatically created (with box) when volume data is loaded into a new molecule (rather than lines). o The color scale range can be customized for the "Index" coloring method New Features o New APBS electrostatic potential interface plugin o Windows versions of VMD now support 3-D texturing used by the "VolumeSlice" representation, and the new color by "Volume" feature. o New "Volume" coloring method, for use with electrostatic potential maps, and other volumetric datasets. Requires OpenGL 1.2 3-D texture mapping. o New "measure sasa" command to measure solvent accessible surface area for an atom selection. New and improved file import and export o Significantly improved Tachyon and POV-Ray output for MSMS surfaces, NewRibbons, and other triangulated surface geometry. o All molecular geometry can now be exported to external renderers that support triangle primitives. o New Wavefront OBJ renderer format for use with tools such as Maya o New PQR file reader/writer plugin o New SYBYL "mol2" reader plugin o New Insight II/Discover "car" reader plugin o New Molecular Discovery GRID volumetric map reader plugin o Updated Charmm coordinate file reader plugin addressing a bug o Updated PSF structure file reader plugin to read PSF files created by CNS 1.1 o Significant DCD trajectory reader performance improvements o The DCD trajectory reader/writer plugin has been udpated to fix a byte swapping problem on Charmm trajectories containing fixed atoms, and now writes files in Charmm/NAMD format by default including unit cell information. o Updated the DX reader plugin to fix a potential problem reading grid lengths, and to use friendlier volume dataset names o Updated the Gromacs readers to allow periodic cells with zero-length periodic cell dimensions o Updated brixplugin, ccp4plugin, edmplugin, and fs4plugin fixing a bug in handling non-orthogonal cells. o All plugins now use common byte swapping code for greatly increased performance reading opposite-endian binary files. In actual use, this results in byte-swapped trajectory reading performance of up to 118MB/sec. General Improvements and Bug Fixes o 20-fold performance increase when rendering volume slice representations on most graphics accelerators. o More than tripled the peak read performance large trajectory files using the "waitfor all" option compared with previous versions. o The 'vmdmovie' plugin now generates movies much more quickly due to new features implemented by the Snapshot and InternalTachyon renderers and improved image format conversion logic. o Atom selection 'set' operations now perform at peak speed without the need to disable display updates or other performance tricks. o Significantly improved the 'points' isosurface representation, selected better defaults for the isosurface representation. o Atom selection performance improvements for "name" and arithmetic evaluation selections. o AutoIMD plugin includes many improvements and bug fixes, and is now more usable with local machines as well as clusters and queuing systems. o Better range checking when writing PDB files from molecules in VMD o Eliminated string copy of residue indices o The Windows joystick code now emits user key events for button presses. o The "FPS" indicator's color can now be changed in the Color window. o Corrected the position of user-defined clipping plane origins Fixed PRs: 420 Known bugs ---------- Visit the VMD page for information on known bugs, workarounds, and fixes: http://www.ks.uiuc.edu/Research/vmd/ Cost and Availability --------------------- BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software Database represent the broad efforts of the Theoretical and Computational Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics, designed to develop and distribute free, effective tools (with source code) for molecular dynamics studies in structural biology. For more information, see: http://www.ks.uiuc.edu/Research/biocore/ http://www.ks.uiuc.edu/Research/namd/ http://www.ks.uiuc.edu/Research/vmd/ http://www.ks.uiuc.edu/Research/jmv/ http://www.ks.uiuc.edu/Development/biosoftdb/ http://www.ks.uiuc.edu/Development/MDTools/ The VMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969). Disclaimer and Copyright ------------------------ VMD is Copyright (c) 1995-2003 the Board of Trustees of the University of Illinois and others. The terms for using, copying, modifying, and distributing VMD are specified in the file LICENSE. If you use VMD in a way you think is interesting or novel, we would like to know about it. The authors request that any published work which utilizes VMD includes a reference to the VMD web page: http://www.ks.uiuc.edu/Research/vmd/ and/or the following reference: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. Documentation ------------- The VMD Installation Guide, User's Guide, and Programmer's Guide are available which describe how to install, use, and modify VMD. All three guides are available from the main web site. Online help may be accessed via the "Help" menu in the main VMD window or by typing help in the VMD command window. This will bring up the VMD quick help page in a browser, and will lead you to several other VMD help files and manuals. Quick Installation Instructions ------------------------------- Detailed instructions for compiling VMD from source code can be found in the programmer's guide. The Windows version of VMD is distributed as a self-extracting archive, and should be entirely self explanatory. The native MacOS X version of VMD is packaged as a disk image and is extracted by opening the disk image, and dragging the "VMD" application contained inside into an appropriate directory. For quick installation of the binary distribution for Unix do the following: 1) Uncompress and untar the distribution into a working directory. In this working directory, there are several subdirectories such as bin, src, doc, data, as well as this README and a configure script. Change to this working directory after the unpacking is complete. 2) Edit the file 'configure'; change the values for the $install_library_dir and $install_bin_dir to a directory in which vmd data files and executables should be installed, be sure that you installing into a clean target directory and not overwriting an existing version of VMD (which would otherwise give problems): $install_bin_dir is the location of the startup script 'vmd'. It should be located in the path of users interested in running VMD. $install_library_dir is the location of all other VMD files. This included the binary and helper scripts. It should not be in the path. 3) A Makefile must be generated based on these configuration variables by running "./configure". 4) After configuration is complete, cd to the src directory, and type "make install". This will install VMD in the two directories listed above. Note that running "make install" twice will print error messages because you are attempting to overwrite some read-only files. Similarly, if you have incorrectly specified the target installation directories or attempt to overwrite an existing VMD installation, you will get error messages. 5) When installed, type 'vmd' to start (make sure the $install_bin_dir directory is in your path). Required Libraries ------------------ VMD requires several libraries and programs for various of its functions. In particular, it uses GL or OpenGL based 3-D rendering, and will require that you have the appropriate GL or OpenGL libraries on your system. Other programs are required by some of VMD's optional features. Please visit the VMD web site for more information: http://www.ks.uiuc.edu/Research/vmd/ For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'. VMD Development Team Theoretical and Computational Biophysics Group University of Illinois and Beckman Institute 405 N. Matthews Urbana, IL 61801 TBG: http://www.ks.uiuc.edu/ VMD: http://www.ks.uiuc.edu/Research/vmd/ README for VMD; last modified December 22, 2003 by John Stone