README file for VMD 1.8.4
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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 and volumetric 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 High-quality on-screen rendering using OpenGL programmable shading on
advanced graphics accelerators.
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 many others, as well as automatic conversion through Babel.
o Export displayed scene to extenal rendering formats including POV-Ray,
Raster3D, Renderman, Tachyon, Wavefront, as well as 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 1.8.4?
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New Platforms Supported:
o Support for Apple MacOS X 10.4 running on Intel based Macintosh computers
o Support for IBM AIX 5.x on 32-bit and 64-bit POWER processors
o Support for Linux running on Itanium based computers (e.g. SGI Prism)
User Documentation Updates
o Updated the URL listed for McKerrell's force field page in various
plugin documentation.
o Fixed missing 'clipplane color' subcommand in User's Guide
o Updated User's Guide text about the MSMSSERVER environment variable
for Windows.
o Significantly expanded documentation pertaining to developing
extensions and plugins in Tcl/Tk, Python, and C/C++.
User Interface Changes
o New '=' hotkey resets/recenters the view on the currently
displayed representations
o File reader/writer plugins are now listed in the graphical interfaces
by a more descriptive name, the scripting interfaces continue to use the
short/terse plugin names with no spaces in them.
o The isovalue slider's range now updates when the selected isosurface rep
is changed and/or the dataset is switched.
o The Isosurface representation now includes a "step" control which
makes it easy to display huge volumetric datasets at coarse resolution
without resampling them first.
o Disable selection text input field for volumetric reps (but preserve
selection text value anyways), since this is not currently used.
o Improved the default search location for 'explorer' on Windows 2000/XP.
New Features
o New "VolMap" extension for creating volumetric density and
occupancy maps from atomic structure coordinates and trajectory data
o New "AutoPSF" extension user interface helps automate structure
building tasks in concert with the 'paratool', 'solvate',
'autoionize', 'membrane', and 'psfgen' structure building modules.
o New BioCoRE collaboratory extension interface allows an already-running
instance of VMD to connect to BioCoRE to publish or display
VMD views stored in the collaboratory.
o New text viewing and editing extension
o New MultiPlot extension takes provides built-in graphing and
plot file export to PostScript and Xmgrace.
o New NAMD Energy extension for calculating energies between atom selections
o New NAMD Plot extension for plotting energies, runtime, memory use
and other data from NAMD simulation log files.
o New NAMD Graphical Interface extension for setting up and running
NAMD simulations.
o Added a "CrystalEyesReversed" stereo mode for projection systems that
are one frame out of phase with the actual stereo sync pulse, such as
the Christie Digital Mirage series projectors.
o New "Beads" representation draws the bounding sphere for each selected
residue, which is useful for displaying very large models at a coarse
level of detail.
o New "Shaded Points" Isosurface rendering mode for fast display of large
volumetric isosurfaces
o New Isosurface "step" size control allows easy subsampling of high
resolution datasets when a crude subsampling method is sufficient
o New "volN" atom selection keyword allows selection of atoms that
correspond to specified voxel values for volumetric datasets
o New "altloc" atom selection keyword allows selections on PDB structures
that contain multiple conformations. VMD doesn't generate bonds between
conformations with different identifiers.
o New 'atomicnumber' and 'element' data fields are provided when structures
are loaded from files containing unambiguous atomic element
information. These new keywords can be used in atom selections.
o New "Element" coloring mode will color atoms by their atomic element
type, when available.
o When atomic element information is available, VMD uses a periodic
table lookup to determine atomic mass and VDW radii, if not it will
guess using the old atom name recognizer heuristic.
o New "measure avpos" command for measuring per-atom average positions
over a trajectory
o New "measure rmsf" command for measuring per-atom RMS fluctuations
over a trajectory
o New "measure sumweights" sum up mass, charge, or one of
the other scalar floating point values efficiently.
New and improved file import and export
o New support for DCD files larger than 2GB on Microsoft Windows
o New support for Charmm DCD files written with 64-bit internal offsets,
as written by Charmm on x86_64 platforms when compiled with -i8.
o New NetCDF-based file reader supporting AMBER 9 trajectories,
and MMTK structure and trajectory files.
o New Biograf (BGF) and extended BGF reader/writer plugins
o New SPIDER volumetric image file reader for loading CryoEM maps
and other volumetric data processed by the SPIDER software
o New Situs volumetric map file reader loads EM maps processed by
the various Situs tools
o New MSMS surface file reader for loading already-calculated MSMS surfaces
o New UHBD potential grid reader plugin
o Updated PDB and WebPDB plugins parse atomic element and alternate
location identifier fields, save all REMARK lines and unrecognized
lines for query by the new 'molinfo top get remarks' command,
and store the database and accession code for query by the new
'molinfo top get database' and 'molinfo top get accession' commands.
o Updated GAMESS plugin supports log files from newer GAMESS versions.
o Updated PSF plugin can write out partial (no angles/dihed/etc) PSF files
with bond records, for use by Situs and other tools.
o Updated Mol2 plugin now writes mol2 files that are compatible with DOCK
o Updated BRIX plugin now aligns correctly with new versions of VMD
o Plugins using the fast I/O routines now use the user's Unix umask
for file permissions when creating new files.
o Fixed a bug in reading coordinates from GROMOS 96 files
General Improvements and Bug Fixes
o New built-in autodetection routine prevents problems with buggy ATI
OpenGL drivers on Linux
o Improved "color by volume" feature now automatically downsamples 3-D
textures to fit within available texture memory on medium-range
graphics boards when possible
o New "serial" atom selection keywords provides one-based atom indexing
for easier conversion of atom indices between VMD and other packages.
o The movie maker plugin now supports user-defined movie types with a
very simple scripting interface that allows researchers to develop
very complex animations. The movie maker now works better when VMD
is installed in a directory name that contains spaces and adds
support for movie rendering with POV-Ray on Microsoft Windows.
o Updated APBS plugin to emit the new syntax for the chgm, srfm, sdens,
bcfl, calcenergy, and calcforce input file parameters to eliminate
warnings with APBS versions 0.4.0 or newer.
o Updated Multiple Alignment plugin fixes incorrect output from the
qpair calculation on Microsoft Windows.
o Force the Inform class to flush its output when sendmsg() is called,
to prevent jumbled output when running VMD as a batch mode job with
intermixed output from the VMD console, Tcl, Python, etc.
o Added new 'gettimestep' command for efficient access to binary
timestep data from Tcl.
o Use boolean for the 'autobonds' suboption of 'mol new' so that values
such as 1, on, true, yes, 0, off, false, and no all work rather than just
1 and 0.
o Fixed volumetric grid aligmnent for CCP4 and DSN6 plugins. They
were scaled in each dimension by an extra factor of N/(N-1).
o Fixed an atom selection leak in the AutoIMD plugin
o Changed OpenGL version number tests to work correctly for video drivers
that advertise themselves as OpenGL 2.0 or later
o Fixed a potential atom selection crash occuring on "within"
atom selections.
o Print a useful error message when problems occur during Python callback
registration
o Added a new vmd_molecule (Tcl) and molecule (Python) callback
to indicate when a molecule was created or its attributes were modified.
Values for vmd_molecule(molid) are:
0: deleted (identical to vmd_initialize_structure(molid))
1: created (though no data is loaded at time of call)
2: renamed
o New Microsoft Visual Studio 2005 project for compiling VMD on
32-bit and 64-bit editions of Windows XP
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) 1995-2006 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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The VMD Installation Guide, User's Guide, and Programmer's Guide
are available which describe how to install, use, and modify VMD.
All three guides are available from the main web site.
Online help may be accessed via the "Help" menu in the main VMD window
or by typing help in the VMD command window. This will bring up the VMD
quick help page in a browser, and will lead you to several other VMD help
files and manuals.
Quick Installation Instructions
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Detailed instructions for compiling VMD from source code
can be found in the programmer's guide.
The Windows version of VMD is distributed as a self-extracting
archive, and should be entirely self explanatory.
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 April 16, 2006 by John Stone