README

CMView 1.1

Interactive Contact Map Visualization and Analysis

http://www.bioinformatics.org/cmview/

INSTALLATION

        You need Java 1.6 or newer (available from http://java.com/en/).

        1. Edit the file cmview.cfg and set the parameters PYMOL_EXECUTABLE and
           optionally DSSP_EXECUTABLE and DALI_EXECUTABLE to point to your local
           PyMol, DSSP and DaliLite executables (CMView will still run without
           this step but some functionality will not be available).

           Free executables for academic use are available from:
           http://sourceforge.net/projects/pymol/files/Legacy/ (Linux, Win, Mac)
           http://swift.cmbi.ru.nl/gv/dssp/ (Linux, Win)
           http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/ (Linux, source code only)

           Please note the individual terms of license for these programs.

        2. To start CMView
           on Windows: run cmview.bat
           on Linux/MaxOSX: run cmview.sh 

        See http://www.bioinformatics.org/cmview/installation.html for more
        information.

THIRD PARTY LICENSE INFORMATION

	CMView uses the following third-party libraries
	which are contained in the CMView download archive:

	1.	File:	 Jama-1.0.2.jar	
		URL: 	 http://math.nist.gov/javanumerics/jama/
		License: Public Domain
		
	2.	File: 	 jaligner.jar
		URL:	 http://jaligner.sourceforge.net/
		License: GPL (http://www.gnu.org/copyleft/gpl.html)
		
	3.	File:	 mysql-connector-java-5.0.5-bin.jar
		URL:	 http://dev.mysql.com/downloads/connector/j/5.1.html
		License: GPL (http://www.gnu.org/copyleft/gpl.html)
		
	4.	File:	 vecmath.jar
		URL:	 https://java3d.dev.java.net/binary-builds.html
		License: GPL with Classpath exception
				 http://www.gnu.org/software/classpath/license.html
		
	5.	Files:   collections-generic-4.01.jar
 				 jung-api-2.0-alpha2.jar
 				 jung-graph-impl-2.0-alpha2.jar
 		URL: 	 http://jung.sourceforge.net/
 		License: JUNG license (BSD)
 				 http://jung.sourceforge.net/license.txt
 		
 	6.	File:	 java-getopt-1.0.13.jar
 		URL:	 http://www.urbanophile.com/arenn/hacking/download.html
 		License: LGPL (http://www.gnu.org/licenses/lgpl.html)
 		
 	7.	File:	 jh.jar
 		URL:	 https://javahelp.dev.java.net/
 		License: GPL with Classpath exception
 				 http://www.gnu.org/software/classpath/license.html
		
	CMView uses icons from the Silk icon set 1.3 by Mark James
	(mjames@gmail.com) which is available under a Creative Commons
	Attribution 2.5 License (http://creativecommons.org/licenses/by/2.5/).
	See: http://www.famfamfam.com/lab/icons/silk/