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Installation

Table of Contents

Quick installation
The details
Setting JVM memory
Secondary Structure and DSSP
DALI structural alignment
Config file

Quick installation

  1. Make sure that Java 1.6 or newer is installed on your machine. If java -version called from the command line reports a version number of 1.6.0 or higher, this is the case. Otherwise, a current version of Java can be downloaded from http://www.java.com/en/download/manual.jsp. You may need to add the bin directory of your Java installation to the path so that CMView can find the java executable.

  2. CMView uses PyMol for 3D molecular visualization. To use this feature you need to have PyMol installed. For the latest features and because PyMol is great software, we recommend to get a sponsor version. A slightly out-of-date free version (0.99) can be downloaded from http://sourceforge.net/projects/pymol/files/Legacy/ or you can compile the latest version from source code.

  3. Download the current version of CMView from downloads.

  4. Unzip the archive. A directory cmview-currentversion will be created.

  5. Edit the cmview.cfg file in cmview-currentversion and set the variable PYMOL_EXECUTABLE to point to your local PyMol executable (see example below). Note that you need to use forward slashes (even on Windows) for the path and no quotes.

    PYMOL_EXECUTABLE=C:/Program Files/PyMol/pymol.exe

  6. To run the program:

    • In Unix and MacOSX: run cmview.sh

    • In Windows: run cmview.bat

  7. Sign up for the user's mailing list to get help and to be notified of updated versions.

The details

Setting JVM memory

By default, the memory for the Java Virtual Machine is set to 256MB. This may be too much or too little depending on your machine and the size of proteins you want to load. You can change this by editing the startup script (cmview.sh or cmview.bat) and setting the -Xmx parameter to a different value. For example:

java -Xmx512m -jar CMView.jar

Secondary Structure and DSSP

By default, secondary structure annotations are taken from PDB files if available. For getting a more consistent secondary structure annotation and to have it in those cases when it is missing in the file, CMView can use the external program DSSP to assign secondary structure. You need to obtain your own licensed copy of DSSP. A free version for non-commercial use can be downloaded from http://swift.cmbi.ru.nl/gv/dssp/. To enable using DSSP in CMView you need to set the parameter DSSP_EXECUTABLE in cmview.cfg to point to your DSSP executable. For example:

DSSP_EXECUTABLE=C:/Program Files/dssp/dssp.exe

DALI structural alignment

In addition to built-in algorithms, you may also locally install DALI to perform structural alignments. See instructions at http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/download.html to install DALI (currently only available for Linux). After installation, add the path to the DALILITE executable in cmview.cfg , i. e.:

DALI_EXECUTABLE=/usr/bin/DaliLite

Config file

There are other configurable parameters that can be set in cmview.cfg. Please refer to the user's manual for a full description.

The configuration file will be read first from the directory where you installed CMView (system-wide config). Per-user customisation is also possible by using a cmview.cfg file placed in your home directory (in Windows that would be something like C:\Documents and Settings\yourusername). Settings in the user configuration file will take precedence over those in the system-wide one.