README file for VMD 1.8.1 --------------------------------------------------------------------------- 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 1.8.1? ------------------------ User Documentation Updates o New figures and updated text documenting new features and differences from past versions of VMD. o Source code documentation is provided online and is updated nightly. User Interface Changes o The Help menu in the main VMD window now provides several direct links to popular documentation topics. o The Tk-based VMD extensions now provide help menu links. o Double-clicking a molecule name bring up the "Rename" dialog. Triple-clicking "T" makes that single molecule T/A/D, resets the view, and selects that molecule in the graphis form. o Forms now consistently refer to "frames" rather than a mix of "frames", "timesteps", etc. o The "Delete Frame" dialog box now clearly states what it is doing (with a message and a "Delete" button), to help users avoid mistakes. o The "NewRibbons" representation has a new spline control. New Features o The "NewRibbons" representation now implements multiple spline types, and has been rewritten to greatly improve overall visual quality. o New periodic cell display feature, useful for viewing molecular dynamics trajectories performed with periodic boundary conditions and simple crystallographic structures. o New built-in TkCon text console plugin with scrolling history, syntax highlighting and many other features. o New user-defined color range controls o New Support for time-varying coloring of molecular geometry with user defined data fields. o New depth cueing controls allow the use of several new depth cueing modes, as well as control over fog density, etc. o New VMDPREFERSTEREO environment variable allows users to override the default behavior of VMD's Unix X11/OpenGL initialization code, favoring stereo visuals over visuals providing antialiasing. o New VMDUSEGALPHA environment variable enables the use of alpha-blended transparency on Unix machines that support it. o Updated Python bindings. o New IMD status display plugin New and improved file import and export o New XYZ file reader plugin o New Gaussian "cube" file reader plugin o New BRIX electron density map reader plugin o New CCP4 electron density map reader plugin o New DSN6 electron density map reader plugin o New STL stereolithography triangulated geometry file reader plugin o Improved PSF file reader with extra safety tests General Improvements and Bug Fixes o The MacOS X version of VMD now utilizes multiple processors and includes a multithreaded Tachyon build. o VMD now uses Tcl and Tk 8.4 for user extensible scripting and graphical interfaces o The "Lines" representation is now faster and looks better due to improvements in rendering code. o The "Points" representation now supports user-selectable point sizes, and implements distance-based point attenuation when on machines where VMD lists "PP" as an available OpenGL extension at startup. o VMD now supports dynamically queried OpenGL extensions as used on Linux, MacOS X, and Windows. o The "backbone" atom selection keyword has been improved so that it excludes atoms in non-nucleic/non-protein residues. o Improved the Tachyon, POV-Ray, RenderMan, and Postscript rendering support, adding depth cueing support, and various tweaks to improve the match between externally rendered scenes and what VMD does with OpenGL. o New "Print" tool for debugging VRPN, CAVE, FreeVR and other 3-D input devices used with VMD. o VMD is now built with Tcl/Tk 8.4.1 Fixed PRs: 176, 189, 198, 220, 246, 247, 249, 251, 252, 254, 259, 260, 262, 263, 264, 265, 266, 273, 283, 294, 296 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 ------------- 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, 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 June 10, 2003 by John Stone