From johns &$at$& ks.uiuc.edu Tue Jun 30 13:53:28 1998 Received: from london.ks.uiuc.edu (london.ks.uiuc.edu [128.174.214.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA05938 Tue, 30 Jun 1998 13:53:27 -0400 (EDT) Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2) id AA273489208; Tue, 30 Jun 1998 12:53:28 -0500 Received: (from johns ( ( at ) ) localhost) by bilbao.ks.uiuc.edu (951211.SGI.8.6.12.PATCH1502/8.6.9)id MAA28647 for chemistry ( ( at ) ) www.ccl.net; Tue, 30 Jun 1998 12:53:27 -0500 From: John Stone Message-Id: <199806301753.MAA28647 <-at-> bilbao.ks.uiuc.edu> Subject: VMD (Visual Molecular Dynamics) 1.2b3 Available To: chemistry ( ( at ) ) www.ccl.net Date: Tue, 30 Jun 1998 12:53:27 -0500 (CDT) X-Mailer: ELM [version 2.4ME+ PL14 (25)] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Announcing version 1.2b3 release of VMD --------------------------------------- The Theoretical Biophysics group at the University of Illinois and the Beckman Institute would like to announce the availability of version 1.2b3 of the program VMD, a package for the vizualization and analysis of biomolecular systems. This software is being made available to the structural biology research community free of charge, and includes the source code for VMD, documentation, and precompiled binaries for SGIs, HPs, Solaris 2, and Linux. The documentation (still being updated) 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. A full description of VMD is available via the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ New in this version ------------------- o VMD now supports AIX 4.x with the native AIX OpenGL implementation o OpenGL rendering speed has been improved by 2-5x on several platforms o OpenGL version now correctly supports stereo-in-a-window o OpenGL/GL versions are now able to interoperate with VMD scripts created in by one or the other. o Upgraded some builds to use newer XForms libraries, which fix some GUI/Mouse bugs o VMD upgraded to compile with the 2.6c release of the CAVE libraries o VMD code now builds with much pickier C++ compilers (i.e. HP aCC) o New Linux binary distributions have working file browser now. o New Linux RPM style binary distribution o New HPUX10-OpenGL binaries for Visualize-FX hardware accelerators o New AIX4-OpenGL binaries for IBM OpenGL hardware accelerators o Many bug fixes Version 1.2b2 features ---------------------- o VMD has been ported to Sun Solaris 2. o Upgraded to support Linux RedHat 5.0 o OpenGL support works with native HP-UX and Sun OpenGL implementations o Added Tk support and upraded to Tcl/Tk 8.0 o Upgraded to Babel 1.6 o Added support for MSMS, a program for calculating molecular surfaces o Added support for Grasp file format o For most commands, typing in a command without arguments will print a help message o Added more commands to Tcl scripting interface o Many bug fixes Version 1.2b1 features ---------------------- o This biggest improvement in version 1.2b1 support for platforms other than GL-based SGIs. In addition to the full source and SGI binary distributions, VMD is now available for HP-UX (tested under 9 and 10) and Linux. o Greatly enhanced Tcl scripting commands for performing molecular analysis, writing scripts, developing tutorials, etc. o New rendering styles, a fast (and cheap) solvent accessible surface and C-alpha and P trace method, and improvements to the existing styles. o New output renderer formats: Postscript, VRML and STL (a stereo-lithography format) o Support for Amber structure and animation file formats ============= Basic information about VMD ================= Features -------- 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, cartoon drawings, 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 limits on the number of molecules, atoms, residues or number of animation frames, excepting available memory. o Many molecular rendering and coloring methods. o Stereo 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, Rayshade, Raster3D, and Radiance. o Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities. o Extensions to the Tcl language 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 describing the source code 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 set up and concurrently display a MD simulation using NAMD. The two programs, along with the intermediary communcations package (called MDComm) constitute the 'MDScope' environment. Availability ------------ The software is available for downloading from http://www.ks.uiuc.edu/Research/vmd/ Please email any questions to vmd # - at - # ks.uiuc.edu. VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools for molecular dynamics studies in structural biology. For more information, see http://www.ks.uiuc.edu/Research/MDScope/. This project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969) and the Roy J. Carver Charitable Trust. John Stone vmd \\at// ks.uiuc.edu June 25, 1998 -- Theoretical Biophysics Group Email: johns \\at// ks.uiuc.edu Beckman Institute http://www.ks.uiuc.edu/~johns/ University of Illinois Phone: (217) 244-3349 405 N. Mathews Ave FAX: (217) 244-6078 Urbana, IL 61801, USA Unix Is Good For You!!!