From owner-comp-bio@hgmp.mrc.ac.uk Fri Jan 12 01:11:17 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0529E17B0D; Fri, 12 Jan 2001 01:11:13 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 0A30917B0C; Fri, 12 Jan 2001 01:11:04 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 205B017AC4; Thu, 11 Jan 2001 21:04:08 +0000 (GMT) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1AECE415F3 for ; Thu, 11 Jan 2001 21:04:01 +0000 (GMT) Received: from teapot30.bigpond.com ([139.134.5.3]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id QAA24133 for ; Thu, 11 Jan 2001 16:03:57 -0500 (EST) Received: (from news@localhost) by teapot30.bigpond.com (8.8.8+Sun/8.8.8) id HAA28159; Fri, 12 Jan 2001 07:52:06 +1100 (EST) To: bionet-biology-computational@moderators.isc.org Message-ID: <3A5E1C1D.775F7472@bigpond.com> From: Mark Addinall Organization: That's IT X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-22 i686) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.biology.computational Subject: Re: Announce: VMD 1.6 Released References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: newsfeeds.bigpond.com 979246265 203.54.194.100 (Fri, 12 Jan 2001 07:51:05 EST) NNTP-Posting-Date: Fri, 12 Jan 2001 07:51:05 EST Date: Fri, 12 Jan 2001 01:11:04 +0000 (GMT) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk 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 .