README file for VMD 1.7 --------------------------------------------------------------------------- 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? ---------------------- New Features o Integrated sequence browsing capabilities are now part of VMD, based on the previously available "ZoomSeq" Tcl script, with many improvements. The sequence browser is significantly faster than the older separately distributed ZoomSeq script, and will eventually provide several new interfaces not included in the production version. o Integrated Ramachandran plotting capabilities are now part of VMD. o Support for joysticks and other game controller input devices on the Windows platforms. o Windows versions of VMD now include support for VRPN, haptic feedback and interactive molecular dynamics. o Unix and Windows versions of VMD now include built-in support for Spaceball 6DOF 3-D controllers, which can be used for rotation, translation, and scaling. The Spaceball can be used simultaneously with the Mouse, so that one can use the mouse for picking, measuring, controlling of user interface menus, while using the Spaceball to orient the molecules in 3D. Future versions of VMD will make the Spaceball interface even more powerful. o New support for OpenGL ARB multisample antialiasing extension, provides multisample antialiasing on Linux/GeForce, Solaris/Expert3D and other platforms. o An easier-to-use -webhelper flag for use with Unix versions of VMD when setting up VMD as a web helper application for PDB files and VMD scripts. General Improvements and Bug Fixes o POV-Ray render export now provides basic support for orthographic views, with other renderers to follow. o Replaced O(N^2) hydrogen-bond finding code with a call to the bond search subroutine, resulting in a 2-4x speedup and better scaling. o Postscript scene exports now includes text labels o The axes are drawn using lines for Mesa builds of VMD. Mesa builds use software rasterization, so axis lines improve display redraws noticably. o Atom selection keywords lookups which operate on integer values now use a hash table to accelerate keyword list processing for a significant speed increase when working with large molecules. o Contains improvements donated by Sergei Izrailev, which make VMD more suitable for use as a library callable from within other applications. o Updated Tcl and Python callbacks to pass shift key state so that scripts like ZoomSeq can do more complex selection and highlighting. o The 'mol pdbload' and 'mol load webpdb' functions now download compressed PDB files from the RCSB, which is both faster and generally more reliable than downloading uncompressed files from the RCSB server. o New "phi" and "psi" angle atom selection keywords, which can be used to query and modify phi and psi angles. o Python commands can now be run with 'gopython -command "foo"' o Added "light pos" commands for setting the position of lights and restoring them to their default values o New "material delete" command o VMD is now built with Tcl 8.3.3 and Tk 8.3.3, which have improved support for secure http and many other omponents. o VMD is now built with Python 2.0.1 o VMD is now built with VRPN 6.0 o Rewritten MSMS interface, fixes PR 20 o Fixed PRs: 20, 157, 158, 159, 160, 161, 162, 163, 164, 165 User Interface Changes o All VMD file browsers are now implemented in Tk by default rather than FLTK, as Tk provides a much better match with the Win32 filesystem conventions. The FLTK file browser did not have a good Win32 interface (no drive letters) so it is now only used as a fall-back when Tk is not compiled into VMD. o The counters for selecting frames in the Edit form now range from 0 to the number of frames for the molecule, looping back to 0 or numframes-1 when the counters hit the end of the valid range. The "Skip" counter was renamed to "Step" and its range was limited to "1" or higher. o New sequence browsing window, and associated menus o Eliminated support for the old XForms GUI toolkit. o IRIX versions of VMD now use xterms instead of winterms, and they use the default font rather than Screen11 which used to cause some problems for people displaying remotely to non-SGI machines. User Documentation Updates o Added documentation for the "frame" atom selection keyword. o New molecular analysis section explaining how to use VMD for common analysis tasks, particularly those involving atom selections and molecule data. o Added documentation for new sequence browsing features o Added documentation for new Ramachandran plotting feature o Added documentation for new Spaceball and Joystick input devices on Windows and Unix. 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 August 1, 2001 by John Stone