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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