README file for VMD 1.8 --------------------------------------------------------------------------- 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). The program 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-based interfaces to Tcl, Tk, and Python to provide powerful scripting and analysis capabilities. o Stereoscopic display and rendering using one of several methods. o 3-D interactive control through the use of joysticks, spaceballs, haptic devices and other advanced input, including support for Virtual Reality Peripheral Network (VRPN). o An extensible plugin-based file loading system with native support for popular formats such as AMBER, CHARMM, Grasp, Gromacs, NAMD, X-PLOR, XYZ, 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 or Protomol 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? ---------------------- User Documentation Updates o Newly updated User's Guide covering all of the new graphical user interfaces, new and updated Python commands, and the many new features. o Source code documentation is provided online and is updated nightly. User Interface Changes o The user interface has been extensively enhanced and revised to be more powerful and easy to use. o Intuitive pulldown menu layout and easier-to-understand menus o New ability to hide/show individual molecular representations with a mouse click o New animation slider bar for easy control of trajectory viewing o VMD now supports wheel mice in the graphics window, for scene scaling. New Features o New "plugin" interfaces for file loading and general extensions o New user-definable atom selection macros allow new atom selection keywords to be defined and saved. o On-the-fly trajectory smoothing with configurable window size o New "DTI SideBySide" stereo mode for DTI flat panel stereo displays. o Up to six user-defined clipping planes can be added to each representation to make cut-away views of molecular geometry. o New dynamically recalculated "dynamic bonds" representation, useful for viewing ab-initio simulations. o New "display resize" command allows script-based display window sizing. o New "Throb" coloring scheme that cycles colors based on wall clock time o Supports the newest version of Tachyon which implements directional lights, orthographic projections, and other VMD-oriented features. Also supports compiled-in "LibTachyon" feature for very fast ray tracings of VMD scenes on IRIX, Linux, and Solaris. o New "measure contacts" and "measure hbonds" commands provide much easier mechanisms for contact and bond searches within scripts. New and improved file import and export o New XYZ file reader plugin o New file loader plugin for NAMD restart files. o New file loader plugin for X-PLOR formatted EDM files. o New AMBER 7 file reader plugins 0 Improved AMBER 6 file reader plugins o VRML2 / VRML97 scene export useful for 3-D printers and other rapid prototyping machines, and web-based visualization of molecular models. o The STL render option now supports representations other than MSMS/Surf. o Improved Renderman RIB exports for Orthographic projections. General Improvements and Bug Fixes o The OpenGL renderer now caches a significant amount of state, eliminating a number expensive OpenGL state manipulation operations which significantly improves rendering performance on multi-display systems. o VMD 1.8 uses several OpenGL extensions and new rendering techniques, all yielding better interactive rendering performance. o Support for Sun XVR-4000 OpenGL video readback extension o The CAVE, FreeVR, and WireGL code have been significantly improved over previous versions. A single binary can now be built with both the CAVE and FreeVR options enabled. o User-defined graphics are now added to existing molecules rather than a separate graphics molecule. This allows annotations highlighting geometry and other data to be attached to a specific molecule. o VMD saved states are now restored much more efficiently. o Colors for atom name and atom type are now assigned based on the first non-numeric character, rather than simply the first character. This makes atoms named 1H3, for example, be colored the same way as othe hydrogen atoms (white), rather than green or some other color. PDB files from the RCSB often have atom names numbers as the first character, but the number carries no information as to how the atom should be colored. o Added a waitfor option to the Tcl animate read/write commands to make them load the specified number of frames (or "all") before returning. o General improvements to the VMD Python documentation and implemention. o Recalculating secondary structure now correctly forces recalculation of colors if the rep is colored by structure. Fixed PRs: 12, 20, 74, 77, 138, 144, 147, 149, 179, 180, 182, 183, 184, 190, 191, 193, 197, 198, 199, 201, 202, 208, 209, 210, 211, 212, 213, 214, 215, 218, 233, 234, 235 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 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) 1995-2002 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 ------------- Three VMD manuals are available which describe how to install, use, and modify VMD. The VMD installation guide, is contained in the VMD distribution in the file "doc/ig.ps". The User's Guide and Programmer's Guide are available separately (due to size) from the VMD web site. Quick help may be accessed by pressing the "Help" button on the main VMD form, or by typing help in the VMD command window. This will bring up the VMD quick help page, and will lead you to several other VMD help files and manuals. Quick Installation Instructions ------------------------------- The Windows version of VMD is distributed as a self-extracting archive, and should be entirely self explanatory. Detailed instructions for compiling this version of VMD can be found in the installation guide. 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: $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. This should be fine. 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 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 8, 2002 by John Stone