README file for VMD 1.2 --------------------------------------------------------------------------- See the section "Installation" of this file for quick information on installing a binary distribution of VMD. 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 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 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 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. What's new in VMD 1.2? ---------------------- o Many updates to VMD documentation o VMD now supports OSF1/Digital Unix 4.x on DEC Alpha with OpenGL or Mesa o Dihedral angles are now reported in the proper range o Various small bug fixes, and portability enhancements What's new in VMD 1.2b4? ------------------------ o Improved display of 3-D axis labels "X","Y","Z". o Fixed POV, POV3, Art, Raster3D, and Rayshade renderer export codes. o Fixed the "write" function found in the "edit animation" dialog. o VMD runs in the Cave simulator now. What's new in VMD 1.2b3? ------------------------ o OpenGL rendering speed has been improved by 2-5x on all 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 VMD now supports AIX 4.x with the native AIX OpenGL implementation 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 What's new in VMD 1.2b2? ------------------------ o Ported to SOLARIS2 o Fixed the problem causing VMD to crash on Linux o Upgraded to HP-UX 10.2 o HP-UX 9.x version is not supported, but VMD can still be compiled o Upgraded to RedHat Linux 5.0, kernel version 2.0.32 o Added Tk support o Upgraded 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 Tcl/Tk help is available through command 'tclhelp' o Added support for insertion codes in PDB files o Added command 'colorinfo index' o Added command 'draw tricolor' o Fixed reading in multiple files o Additions to the 'configure' script for compiling with various options o A few bug fixes What's new in 1.2b1? -------------------- o New "Solvent" representation for a fast/cheap surface o New "Trace" representation o Tube now works for structures with only C and/or P atoms o Additional selection keywords o Improved Tcl callbacks (VMD now requires compiling with Tcl) o Alt- and Ctrl- hotkey modifiers o Read and write Amber molecule and animation file formats o More renderers (VRML, STL, Postscript) o Support for non-SGI platforms using Mesa to emulate OpenGL o Compiles with g++ o Many bug fixes Known bugs ---------- o OpenGL and the XForms menus sometimes conflict - A form must have been open at least once before using the pop-up menu from the graphics screen. Otherwise pressing the right mouse button in the graphics form will cause VMD to exit and report a X problem. - The popup is in a different colormap than the OpenGL display, but the colormap doesn't switch when in use o Colormap flashing on 8-bit color systems o The default window size information doesn't always work o DCD binary format is platform specific and Intel doesn't work the same as MIPS,Sparc,PA-RISC etc (which do have the same format). We have a workaround for this problem. If you need a program which fixes the endianism of DCD files, please send us mail. o There are sometimes small unwanted gaps in the connections between tubes and beta sheets, and between tubes in the "cartoon" representation. o The depth cue and antialias GUI buttons don't always work. The cause of these problems has been determined, and they are being addressed for future releases of VMD. Cost and Availability --------------------- VMD, NAMD, and the entire MDScope environment are part of an ongoing project within the Theoretical Biophysics group to help provide free, effective tools (with source code) 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 RR05969-04) and the Roy J. Carver Charitable Trust. Disclaimer and Copyright ------------------------ VMD is Copyright (c) 1995-1998 Theoretical Biophysics Group and the Board of Trustees of the University of Illinois Portions of VMD code are Copyright (c) 1997-1998 Andrew Dalke 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. Please take a few minutes to fill out a registration form at http://www.ks.uiuc.edu/Research/vmd/VMDregistration.html if you are going to use VMD. 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. Some of the code and executables used by VMD have different restrictions. They are: 1) STRIDE, the program used for secondary structure calculation, is free to both academic and commercial sites provided that STRIDE will not be a part of a package sold for money. The use of STRIDE in commercial packages is not allowed without a prior written commercial license agreement. See the Stride WWW page at: http://www.embl-heidelberg.de/stride/stride_info.html 2) Det, Eigen, and Invert are part of the LASSTools package from Cornell. See http://www.lassp.\\cornell.edu/LASSPTools/LASSPTools.html The executables may be redistibuted to other users. Note that this redistribution may not be done for a fee (other than a material media charge, if necessary). Ownership resides with the authors of the programs. 3) The source code for SURF is copyrighted by the original author, Amitabh Varshney, and the University of North Carolina at Chapel Hill. Permission to use, copy, modify, and distribute this software and its documentation for educational, research, and non-profit purposes is hereby granted, provided this notice, all the source files, and the name(s) of the original author(s) appear in all such copies. BECAUSE THE CODE IS PROVIDED FREE OF CHARGE, IT IS PROVIDED "AS IS" AND WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED. This software was developed and is made available for public use with the support of the National Institutes of Health, National Center for Research Resources under grant RR02170. ftp://ftp.cs.unc.edu/pub/projects/GRIP/SURF/surf.tar.Z 4) The perl script to retrived web documents, url_get, was written by Jack Lund at the University of Texas as Austin. There appear to be no restrictions on its use. 5) Several parts of the GNU C++ class library are used in VMD, including the String and Regex classes, alloca, and librx regular expression library. As per the GNU Library General Public License v. 2, the modified code is available as part of the general VMD source distribution and may be freely used and altered. Feedback -------- We would like to know who is using our software both for our own knowledge and to support our funding. If you find VMD useful or want to make comments, please fill out our on-line feedback form at http://www.ks.uiuc.edu/Research/vmd/VMDfeedback.html . Documentation ------------- Three postscript documentation files are available for VMD which describe how to install, use, and modify VMD. One, the installation guide, is contained in the VMD distribution in the file doc/ig.ps . The other two, the User's Guide and Programmer's Guide are available independently from the VMD distribution directory as ug.ps and pg.ps . A quick help file in HTML format, 'vmd_help.html' is also available, in the 'data' directory of the distribution. This file may be viewed by any HTML viewer, and is used to provide on-line help for VMD when it is running. This file is outdated and does not contain information beyond version 1.0 . For the latest information on VMD, please see the VMD WWW home page: http://www.ks.uiuc.edu/Research/vmd/ This page contains links to HTML versions of all three VMD manuals listed above, and info on the latest release of the program. A brief VMD FAQ is also available, and can be found either by looking at the VMD home page, or directly via the URL: http://www.ks.uiuc.edu/Research/vmd/vmd_faq.html Installation ------------ Detailed instructions for compiling this version of VMD can be found in the installation guide, ig.ps. For quick installation of the binary distribution (for IRIX, HPUX, Solaris, and Linux), 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) The proper Makefile must be generated based on these configuration variables. This is done 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 ------------------ The VMD binary distributions available from this site rely on a number of basic system services in order to function. In particular, VMD requires a functionally complete X-Windows installation, and if using one of the binaries built with vendor provided OpenGL libraries, it may additionally require that the vendor OpenGL libraries, GLX windowing system extensions and related software be properly installed on your system. Below is a list of the vendor provided OpenGL runtimes that must be installed for the matching VMD binaries to run correctly: o VMD with Sun OpenGL: Requires that the Sun OpenGL runtime is installed The Sun native OpenGL version will only execute on UltraSPARC, as these are the only systems which support hardware accelerated rendering with Sun's implementation of OpenGL. Non-UltraSPARC systems should use the Mesa version of VMD. o VMD with HP OpenGL: Requires that the HP OpenGL runtime is installed The HP native OpenGL version will only execute on PA-8x00 series processors, as these are the only systems which support the Visualize FX series hardware accelerators. Non-PA-8x00 systems should use the Mesa version of VMD. 0 VMD with IBM OpenGL: Requires that the IBM OpenGL runtime is installed For information on related programs see http://www.ks.uiuc.edu/Research/vmd/related_programs.html For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'. A. Dalke, W. Humphrey, S. Izrailev, J. Stone, J. Ulrich Theoretical Biophysics Group University of Illinois and Beckman Institute 405 N. Matthews Urbana, IL 61801 TBG WWW: http://www.ks.uiuc.edu/ VMD WWW: http://www.ks.uiuc.edu/Research/vmd/ General README for VMD; last modified June 26, 1998 by John Stone