README file for VMD 1.7

What is VMD?            See also
  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:

  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:

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 
  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 
    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 

  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:

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:

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:

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.

  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/". 
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:

For problems, questions, or suggestions, send e-mail to ''.

  VMD Development Team
  Theoretical Biophysics Group
  University of Illinois and Beckman Institute
  405 N. Matthews
  Urbana, IL  61801

README for VMD; last modified August 1, 2001 by John Stone