README file for VMD 1.8.1
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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).
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?
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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
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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 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
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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
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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, 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
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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 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