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Tutorials and Examples

Installing and using Shake'n'Bake 2.1 (SnB) Dual-space direct methods software on Redhat Linux 6.x (and Mandrake 7 Linux)

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] |

Main Problem: Installing the right Java Run Time for Linux

The main complication of getting SnB working on Linux is using a solid Java Run Time engine. For SnB 2.1, you need to install JDK 1.1.8 available from http://www.blackdown.org. This can be a minor dog of a thing to get installed. But once done, things go quite smoothly on the SnB side of things. Extra links are provided so you can easily find other information if you strike problems.

If you have Kaffee Java Run Time Engine installed, deinstall it (The SnB GUI does not work with this Java Run Time Engine).

An example of doing this on Redhat Linux 6.2: as root run the Kpackage program, browse to Development, Languages, Kaffe, the click on the bottom middle Uninstall ICON.

Installing bzip

So you can install the bzipped JDE, obtain bzip2 and install this extraction software. Do a chmod +x bzip to make it executable after the download.

Obtain and Install the JDK and JRE 1.1.8 Java Run Time Engine

Put the jre118_v1-glibc-2.1.2.tar.bz and jdk118_v1-glibc-2.1.2.tar.bz into the /usr/local directory and use the following commands to extract:

  • bzip2 -d < jre118_v1-glibc-2.1.2.tar.bz | tar xvof -
  • bzip2 -d < jdk118_v1-glibc-2.1.2.tar.bz | tar xvof -
Set the following environment variables for both Java and SnB:

Bash Shell (not healthy for Platon/System S) (edit the .bashrc file)

  • export JAVA_HOME=/usr/local/jdk118_v1
  • export SNB_BIN=/usr/local/bin/snb2.1/bin
  • export PATH=$JAVA_HOME/bin:$SNB_BIN:$PATH
  • export CLASSPATH=.:$JAVA_HOME/lib/classes.zip

Cshell (tsh/csh) Shell (recommended for Platon/System S) (edit the .cshrc file)

  • setenv JAVA_HOME "/usr/local/jdk118_v1"
  • setenv CLASSPATH "/usr/local/jdk118_v1/lib/classes.zip"
  • set lpath = ( /usr/local/jdk118_v1/bin /usr/local/bin/snb2.1/bin )
  • set path = ( $lpath $path )

Obtaining and Installing Snb (Shake'n'Bake)

(Assumes you have the appropriate Java Run Time already installed)

Other mirrors of the SnB site exist though the executables are still downloaded from the primary home site in the USA:

SnB download page:

Go to the SnB (Shake'n'Bake) download area and select the "SnB v2.1, academic and other nonprofit users" version of SnB.

Unless unacceptable, accept the usage agreement version. Put in your contact information and download the tar.gz file for your relevant system.

To extract the tar.gz file (in this case using the SGI executable as an example), type

gzip -d < snb2.1-sgi.tar.gz | tar xvof -

To install, go into the resulting snb-temp directory and type ./Install to install. The SnB installer will test for a Java engine, bring up a graphical window and you press Next to continue on with the installation. (if you installed the Java Run Time just prior to this, make sure the environment statements have been applied so that the SnB installer will recognise that Java has been installed)

Enter which directory you would like SnB to be installed into. (or accept the default). The files will be extracted. DONE!

If installing into a general area as root (e.g., in /usr/local/bin/snb2.1), make sure all the files are readable by general users by doing:

chmod -R +r /usr/local/bin/snb2.1/*

If you do not do this, ordinary users may only get a grey image that goes no further when they run SnB.

So you can run SnB from any directory, put it's path in your shell config file (this information is also given above). E.g., for the csh,

set path=(/usr/local/bin/snb2.1/bin $path)

If using csh, "rehash", then re-"source" your .cshrc file (or logout then log back in) for this to take affect.


source .cshrc


There are example files in the following distribution directory.

I.e., /usr/local/bin/snb2.1/examples

A possible good quick example to try out is in the following directory

I.e., /usr/local/bin/snb2.1/examples/Basic/28-atom

SnB on-line tutorial and advice pages:

Main SnB Tutorial Page

Tutorial Main page on the SnB GUI (just keep clicking on Next to continue)

Tutorial guide to optimising the SnB options to your structure problem (just keep clicking on Next to continue)

Example screen dumps of SnB running on an example structure.

To run SnB, type SnB and follow the program flow via the Java based GUI

[Tutorials page] | [Platon Index]

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