README file for VMD 1.7.1 --------------------------------------------------------------------------- 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 a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. 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 Stereoscopic display capability using Red/Blue or LCD shutter glasses. o 3-D interactive control through the use of joysticks, spaceballs, haptic devices and other advanced input, including support for the UNC Virtual Reality Peripheral Network (VRPN) system. o Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more). o Ability to write the current image to a file which may be processed by a number of popular raytracing and image rendering packages, including POV-Ray, Radiance, Raster3D, Rayshade, and Tachyon. o Integration with the program 'Babel' which allows VMD to read many molecular data file formats. Even without the use of Babel, VMD can read PDB files, as well as CHARMM- and X-PLOR compatible binary DCD files and X-PLOR compatible PSF files. o Extensive graphical and text-based user interfaces, which use Tcl, Tk, and Python to provide powerful scripting capabilities. o Built-in extensions to the Tcl and Python languages which enable researchers to write their own routines for molecular analysis. o Modular, extensible source code using an object-oriented design in C++. o Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical Biophysics Group at the University of Illinois. See the NAMD WWW home page for more information: http://www.ks.uiuc.edu/Research/namd o VMD can be used to interactively display and control an MD simulation using NAMD or Protomol. o Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that BioCoRE collaborators can work together over the internet. See the BioCoRE WWW home page for more information: http://www.ks.uiuc.edu/Research/biocore What's new in VMD 1.7.1? ------------------------ New Features o New volume rendering features including isosurface display, volume slicing with support for hardware accelerated 3-D texture mapping, and a Tcl volume data loader interface. o Support for scanline-interleaved stereoscopic rendering for hardware such as the Eye3D stereo glasses and decoders. These work on Linux, Windows, and most any other platform with VGA and USB connectors, and they don't require any special software in order to work with VMD. o First inclusion of VMD plugin architecture. Initially used to provide the structure building capabilities of psfgen in VMD. o Added "mol selupdate" and "$sel update" commands. "mol selupdate" ' causes automatic updates of the selection for the specified representation. o The Windows version of VMD can now be run from a command line with the use of the Windows "start" command, i.e. something like "start c:\vmd\vmd.exe -nt -e myscript.vmd" could be used to start VMD if it were installed in directory c:\vmd. General Improvements and Bug Fixes o Includes a much faster version of Stride for secondary structure calculation. o Includes new version of the Tachyon ray tracer, 0.93.4. o Multi-level OpenGL stipple-based "screen door" transparency. Now implements varying levels of transparency. o Improved support for WireGL cluster-based rendering and tiled display walls. o The IMD code now closes down active socket connections more carefully, allowing the kernel to complete any in-progress write operations before closing the socket. o POV-Ray scene export improved with new camera parameters and support for orthographic views, shadow control, and matched perspective camera views. o Tachyon scene export improved with new camera parameters for matched perspective views with VMD. o Raster3D scene export improved with new camera parameters for matched perspective views with VMD. o The Windows version of VMD now reads "vmd.rc" for startup instead of ".vmdrc". This makes it much easier to edit the startup files on Windows. o Replaced DNA example molecule with a better one. o H-bonds shown in the H-bond rep are now pickable. o Added code to read the unit cell data from Charmm trajectory files. o Improved robustness and error handling when reading Raster3D scene files. Fixed Raster3D file reading crash. o The "delete" option for atom selections no longer leaks memory in the case when it is used within a Tcl loop. o Eliminated atom selection and Tcl related memory leaks Fixed Bugs and PRs: 107, 168, 170, 171, 172, 173, 174, 177, 178 User Interface Changes o Users can select either FLTK or Tk file browsers according to their personal preference. Some people prefer the Windows-like function of the Tk browsers, while others like the filename completion of the FLTK file browser. This is configured by setting the VMDFILECHOOSER environment variable. The default browser for Windows is the Tk browser, for Unix systems the FLTK browser is the default. o Reverted behavior of the edit form old "-1" index use. User Documentation Updates o New manual section for the sequence window o Updated sections regarding .vmdrc since Windows now uses vmd.rc instead. o Updated the betacolor example script included in the docs for new versions of VMD. o Updated the animation scripts in the script library for new versions of VMD. o Improved index entries pertaining to lighting and shading. Known bugs ---------- Please visit the VMD web site 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/Development/biosoftdb/ http://www.ks.uiuc.edu/Development/JMV/ 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) 1995-2001 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. 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 23, 2001 by John Stone