README file for VMD 1.8
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What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/
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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?
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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
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Visit the VMD page for information on known bugs, workarounds, and fixes:
http://www.ks.uiuc.edu/Research/vmd/
Cost and Availability
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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
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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
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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
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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
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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