VMD README file for version 1.2b1
---------------------------------------------------------------------------

See the section "Installation" of this file for quick information on
installing a binary distribution of VMD.

                         NOTE FOR FTP USERS
                         ------------------
The VMD ftp directory (ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd/) contains
several different versions of the VMD distribution.  They are:

  The complete source:
    vmd-1.2b1.all.tar.gz

  Precompiled binaries for different platforms
    vmd-1.2b1.bin.IRIX5.tar.gz
	Works for IRIX 5.x and 6.x using GL
    vmd-1.2b1.bin.HPUX9.tar.gz
	Works for HP-UX 9 and HP-UX 10 using Mesa emulated OpenGL
    vmd-1.2b1.bin.LINUX.tar.gz
	Tested under RedHat with 1.2.13 and 2.0.27 kernals, uses Mesa

  Versions for other operating systems may also be available.  All
files are compressed using the "gzip" program.  We no longer
distribute a .Z version.  Precompiled version of "gunzip" are
available for your platform at ftp.netscape.com in the directory
/pub/unsupported/gnu/ .


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 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

Why is it "b1"? or, What's wrong with this version?
--------------------------------------------------

  This is the first version of VMD for OpenGL and for non-SGI
platforms.  As such, we haven't been able to test the different
versions as much as we would expect.  Excepting the bugs listed below,
there are no unusual problems with the non-IRIX5 versions.  If you
come across one, please inform us so we can correct it.

	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
	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 or PA-RISC

  These problems don't exist on SGIs because that implementation still
uses GL.  We know of no bugs for the SGI version.


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 National Science Foundation (grant number BIR-9318159).

Disclaimer and Copyright
------------------------

    VMD is Copyright (c) 1995-1996 Theoretical Biophysics Group and
the Board of Trustees of the University of Illinois

    This program is free software but is not in the public domain.  It
is distributed in the hope that it will be useful to the molecular
modelling community, but WITHOUT ANY WARRANTY; without even the
implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.  Should the software prove defective YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

Permission is granted for research, educational, and commercial use
and modification so long as 1) VMD and any derived works are not
redistributed for any fee, other than media costs, 2) proper credit is
given to the Theoretical Biophysics group for their work, and 3)
programs derived from VMD must by given a different name.  If you use
VMD in a way you think is interesting or novel, we would like to know
about it.

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
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.

See 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.

See http://uts.cc.utexas.edu/~zippy/projects/url_get/ .

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 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, 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.parameters'; change the value for
the INSTALLLIBDIR to a directory in which vmd data files and executables
should be installed, and change the following values:

	INSTALLBINDIR is the location of the startup script 'vmd'.  It
should be located in the path of users interested in running VMD.

	INSTALLLIBDIR 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 put the code 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
INSTALLIBDIR directory is in your path).


For problems, questions, or suggestions, send e-mail to 'vmd@ks.uiuc.edu'.

	A. Dalke, W. Humphrey, 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/

Special thanks for this release goes to Steve Searle for helping out
with OpenGL.
  

General README for VMD; last modified March 24, 1996 by Andrew Dalke.