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/