Announce: VMD 1.6 Released

Mark Addinall mark.addinall at bigpond.com
Thu Jan 11 20:11:04 EST 2001


John Stone wrote:

Thanks very much.  I seem to be having all sorts of
trouble getting it to run under RedHat 7.0

Anyone else tried this>

Mark Addinall


> 
>          VMD "Visual Molecular Dynamics" 1.6 Announcement
>          ------------------------------------------------
> The Theoretical Biophysics group at the Beckman Institute For Advanced
> Science and Technology, the University of Illinois (U-C), is proud to
> announce the public release of VMD 1.6.  VMD is a package for the
> visualization and analysis of biomolecular systems.  This software is
> distributed free of charge and includes source code, documentation,
> and precompiled binaries for Compaq, IBM, HP, Linux, Sun, and SGI Unix
> systems, as well as Microsoft Windows 95/98/ME/NT/2K.
> The VMD documentation includes an installation guide, a users guide, and a
> programmers guide for interested researchers.  VMD also provides on-line
> help through the use of an external HTML viewer.  VMD development is
> supported by the NIH National Center for Research Resources.
> 
> A full description of VMD is available via the VMD WWW home page:
>         http://www.ks.uiuc.edu/Research/vmd/
> 
> 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.
> 
> The Theoretical Biophysics group encourages VMD users to be closely
> involved in the development process through reporting bugs, contributing
> fixes, periodical surveys and via other means.
> 
> We are eager to hear from you, and thank you for using our software!
> 
>                                                 John Stone
>                                                 vmd at ks.uiuc.edu
>                                                 December 22, 2000
> 
>                        README file for VMD 1.6
> ---------------------------------------------------------------------------
> 
> 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.
> 
>   o Extensive atom selection syntax for choosing subsets of atoms for
>     display (includes boolean operators, regular expressions, and more).
> 
>   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 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 Extensive graphical and text-based user interfaces, which use the
>     Tcl package to provide full scripting capabilities.
> 
>   o 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++, with a programmer's guide outlining the source code structure.
> 
>   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 info:
>       http://www.ks.uiuc.edu/Research/namd
> 
>     VMD can be used to interactively display and control an MD simulation
>     using NAMD.
> 
> What's new in VMD 1.6?
> ----------------------
>   New Features
>     o New "mol load webpdb XXXX" internet based PDB loading on both
>       Windows and Unix platforms.
>     o Python scripting interface available on Linux, Solaris, and IRIX versions
>     o Wireframe rendering modes for MSMS and Surf (new control counter on
>       the MSMS/Surf rep subforms)
>     o Support for generation of RenderMan .RIB files from VMD scenes.
>     o New platform support for Linux on Alpha processors
>     o New platform support for Linux on PowerPC processors
>     o Improvements supporting "VMD chat", a Tcl based collaborative VMD
>       session feature to allow two or more people to connect their VMD
>       sessions over a network.  The "VMD chat" script is provided in
>       the VMD script library.
>     o Improvements supporting "ZoomSeq" sequence-based highlighting,
>       selection, and coloring, as well as rudimentary internet based sequence
>       search/query through new Tcl scripts, also to be found in the VMD
>       script library soon after VMD 1.6 is released.
> 
>   General Improvements and Bug Fixes
>     o Windows version of VMD now implements mouse capture so that you can
>       drag the mouse outside of the graphics window while doing rotations,
>       translations, scaling, and other mouse dragging operations.
>     o Improved interactive rendering speed of molecular surfaces by a factor
>       of two or more on most platforms.
>     o Improved OpenGL materials rendering and gave VMD better looking
>       default material properties.
>     o Tachyon ray tracer binaries are now packaged along with VMD on all
>       supported platforms.  Now includes faster version of Tachyon.
>     o Added the ability for Tcl code to capture VMD events as through
>       the logfile mechanism, but through a Tcl variable, so that one VMD
>       can easily remote control other VMD's through a bit of Tcl sockets code.
>     o Significant speed increases for many common VMD commands,
>       many commands are 5 to 200 times faster now, using new Tcl 8.x
>       interpreter interface.
>     o Made it easier to customize size/position of the VMD command window
>       on Unix versions of VMD.
>     o Improved VMD startup script, now works beter on HP-UX systems
>     o No longer built with TclX/TkX, these are now removed from distribution.
>     o Trimmed out excess baggage in VMD scripts directory
>     o Built with FLTK 1.0.9
>     o Built with VRPN 5.01
>     o Fixed PRs: 60, 101, 106, 108, 109, 110, 111, 112, 113, 114, 124
> 
>   User Interface Changes
>     o New Tcl/Tk based RMSD fit GUI
>     o Save state uses a GUI dialog now when possible.
>     o The representation browser in the graphics form no longer lists the
>       numbers associated with a draw style, to conserve space and improve
>       readability.
> 
>   User Documentation Updates
>     o Doucmentation for new Python scripting interfaces.
>     o Updated various sections in User's guide, particularly relating to new
>       rendering features, RMSD fit, etc.
>     o Started lengthy update to Programmer's guide.
>     o Added commit email capability to CVS, may make it an option
>       for read-only CVS users as well.
>     o significant improvements to Tcl scripting section
> 
> 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
> ---------------------
>   VMD, NAMD, and BioCoRE 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/VMD/
>   http://www.ks.uiuc.edu/Research/NAMD/
>   http://www.ks.uiuc.edu/Research/biocore/
> 
> The VMD project is funded by the National Institutes of Health
> (grant number PHS 5 P41 RR05969).
> 
> Disclaimer and Copyright
> ------------------------
>   VMD is Copyright (c) 1995-2000 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 at 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 22, 2000 by John Stone
> 
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns at ks.uiuc.edu                 Phone: 217-244-3349
>   WWW: http://www.ks.uiuc.edu/~johns/         Fax: 217-244-6078







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