===============================================================================

		      MGLTOOLS 1.5.7 version 
			BINARY DISTRIBUTION

===============================================================================

Thank you for downloading MGLTools.

This distribution contains a pre-compiled Python interpreter (version 2.7),
a collection of pure Python packages (including Pmv, AutoDockTools, 
DejaVu, MolKit, ViewerFramework, Vision, NetworkEditor, CADD, etc.), various 
platform dependent packages (including mslib, opengltk, bhtree, gle, 
sff, cAutoDock, UTpackages, etc.), and the PMV, ADT and VISION applications 
built on top of these software packages.


**************************************************************************
**  CITING THESE TOOLS IN PUBLICATIONS
**************************************************************************

Whether you downloaded the Academic or the Commercial distribution, we ask 
that you acknowledge using these tools in any publications arising from their 
use. 
Under the PMV Help menu there is a citation command providing various
papers to be cited for various tools included in this distribution.

	PMV  Help->citations

more license information is available below


**************************************************************************
**  INSTALLATION
**************************************************************************

    PREREQUISITES                
    ------------
       	- OpenGL version 1.2 or higher is required for using VolumeRendering 
        tools available in VISION and PMV.
	- For Mac OS X machines, X11(an implementation of the X Window System)
          is required.
	- This distribution is self contained and will not interact with
        any other python interpreter installed on your machine.

    If you downloaded the tar file:
    -----------------------
    1.

	tar -zxvf mgltools_i86Linux2_1.5.7.tar.gz


    2. Run the installation script.
	   > ./install.sh [options]

	   The installation script can be used with the following options:
             [-d InstDir]      specifies installation directory 
                               (default-current directory)

             [-c optimization] optimization option for compiling Python code
                               0 - no optimization (generates .pyc files)
    		               1 - with optimization (generates .pyo files);

	     [-h]              help message.


	The installation script installs MGLTools in
	InstDir/MGLToolsPckgs .
        
	It also creates various shell scripts (pmv, adt, vision, pythonsh)
	in InstDir/bin. 


  RUNNING ADT, PMV or VISION
  --------------------------

  To be able to start any of these applications you will need to:

  - either add "InstDir/bin" to the path environment variable in your 
   .cshrc or .bashrc as in the following example:

     .cshrc on Linux 
     set path = (InstDir/bin $path)

     .bashrc on Linux
     export PATH="InstDir/bin:"$PATH

  - or create aliases in your .cshrc or .bashrc as in the next examples:

     .cshrc on Linux:

     alias pmv InstDir/bin/pmv
     alias adt InstDir/bin/adt
     alias vision InstDir/bin/vision
     alias pythonsh InstDir/bin/pythonsh

     .bashrc on Linux:

     alias pmv='InstDir/bin/pmv'
     alias adt='InstDir/bin/adt'
     alias vision='InstDir/bin/vision'
     alias pythonsh='InstDir/bin/pythonsh'

 - or run the following script that is created at installation:
      source ./initMGLtools.sh 
                          (bash) 
      source ./initMGLtools.csh 
                          (c-shell)


  To use PMV, ADT or VISION type pmv, adt or vision respectively; 

	for example:

	> pmv 

	A Python Molecule Viewer should come up.  
 	You can load files from the "Data" directory and start playing with 
	PMV.  

      To run Python interpreter type "pythonsh":

	> pythonsh


	
  Mac OS X INSTALLATION
  ---------------------
  The Mac OS X version of MGLTools requires some form of X11 server to 
be installed. Apple X11 is available for downloading at 
http://developer.apple.com/opensource/tools/runningx11.html.

MGLTools for Mac OS X are available in a disk image file format
(with the extension ".dmg"). This file contains Mac OS X installer 
created by PackageMaker.
 NOTE: To install this package the user has to be logged in as root. 
  - download mgltools_#platform#_1.5.7.dmg file;
  - double-click on the resulting ".dmg" file;
  - double-click on the package file ".pkg" and follow the instructions given by    the installer;

The installer installs MGLTools packages in /Library/MGLTools .

The following applications are installed in /Applications folder: 
PMV, AutoDockTools, Vision
Vision Icon
Double-click on the PMV, AutoDockTools or Vision icon to start the application.


**************************************************************************
**  Pmv script command line options
**************************************************************************

"pmv" script can be used with the following options:

        -h or --help       : print help message
        -a or --again      : play back lastlog file
        --overwriteLog     : overwrite log file
        --uniqueLog        : create a log file with a unique name
        --noLog            : turn off logging
        --noGUI            : start PMV without the Graphical User Interface
        --noSplash         : turn off Splash Screen
        --die              : do not start GUI event loop
        --customizer file  : run the user specified file
        --lib packageName  : add a libraries of commands
        -v r or --vision run  : run vision networks on the command line
        -v o or --vision once : run vision networks and exit PMV

        --update [nightly|tested|clear] : update MGLTools
                if no arguments are given Update Manager GUI is provided
                'nightly': download and install Nightly Builds
                'tested' : download and install tested Nightly Builds
                'clear'  : clear/uninstall all the updates

	-d or --dmode modes : specify a display mode
	        modes can be any a combination of display mode
		   'cpk'  : cpk
		   'lines': lines
		   'ss'   : secondary structure ribbon
		   'sb'   : sticks and balls
		   'ms'   : molecular surface
		   'ca'   : C-alpha trace
		   'bt'   : backbone trace
		   'sp'   : CA-spline
		   'sssb' : secondary structure for proteins,
		            sticks and balls for other residues with bonds
			    lines for other residues without bonds

	-c or --cmode modes : specify a dispaly mode
                color scheme:
		    'ca' : color by atom
		    'cr' : color by residue (RASMOL scheme)
		    'cc' : color by chain
		    'cm' : color by molecule
		    'cdg': color using David Goodsell's scheme
		    'cs' : color residues using Shapely scheme
		    'css': color by secondary structure element
	'-i', '--interactive' : PMV interactive shell


 EXAMPLE::
     Display protein as ribbon, non protein as sticks and balls
     and color by atom type
	         pmv -i --dmode sssb --cmode cr myprot.pdb
	         pmv -i -m sssb -c cr myprot.pdb 
 	

**************************************************************************
**  LICENSES
**************************************************************************

You can refer to the license information available for the following packages:

   -Python packages developed at MGL(Pmv, DejaVu, ViewerFramework, 
    AutoDockTools, MolKit, NetworkEditor, Vision, PyBabel, mglutil): 
        ./LICENSES or  http://mgltools.scripps.edu/downloads/license-agreements

   -Platform dependent packages:
      -- mslib - library to compute molecular surfaces,
      ./LICENSES or http://www.scripps.edu/~sanner/python/tsrilicense.html

Unless otherwise stated, packages that do not specify a license are released 
under the MOZILLA Open Source License.



**************************************************************************
**  DOCUMENTATION
**************************************************************************

Documentation, tutorials and more information are
available online:
 http://mgltools.scripps.edu/documentation

**************************************************************************
**  HOW TO CONTACT US:
**************************************************************************

Several mailing lists are available for asking questions and getting answers
You can subscribe or search the archives of these lists at:

	http://mgldev.scripps.edu/mailman/listinfo

The following lists are relevant to this distribution
 
 -autodock: a community of AutoDock, AutoGrid and AutoDockTools (ADT) users 
  with lots of experience to share
  http://mgldev.scripps.edu/mailman/listinfo/autodock

 -pmv for questions regarding the use of PMV;
  http://mgldev.scripps.edu/mailman/listinfo/pmv

 -vision for questions regarding the use of VISION;
  http://mgldev.scripps.edu/mailman/listinfo/vision

 -MGLTools support for questions regarding installing the MGLTools.
  http://mgldev.scripps.edu/mailman/listinfo/mglsupport

Please visit our Frequently Asked Questions page if you have any problems 
installing or running our tools (http://mgltools.scripps.edu/documentation/faq).
For other inquiries, send an email to mgltools:
 mgltools@scripps.edu



