This page provides a very brief introduction to BioShell set-up. More information can be obtained from Installation page on this website.

Installation in brief

  • Check if you have JAVA Run Time Environment installed on your machine. It is very likely that you have. If not, download it from Sun website and install.
  • Install Jython scripting language. This looks similar to the previous point. You need to download an installer from this website and launch it.
  • Download BioShell and copy the jar archives to a destination directory.
  • Put the jar files on your CLASSPATH variable

Running BioShell programs

Now you can use BioShell command-line programs. For example you can calculate crmsd distance between two proteins structures (PDB files) using RmsCalc tool:

java RmsCalc -qp=model1.pdb -tp=model2.pdb

To learn more on BioShell command-line tools, have a look on Programs page.

Running BioShell scripts

Once you installed Jython you can also launch BioShell scripts. If your script is located in a working directory, you can type:

jython histogram.py

Otherwise it is necessary to provide a path:

jython ./jbcl/examples/jython/calc/statistics/histogram.py

Obviously you can pass arguments to scripts, e.g.

jython carbonyl_improper_angle.py pdb2gb1.ent.gz

The two examples abowe assume that path to jython executable is listed in your PATH environmental variable. This may be simply done by editing one of your startup scripts, e.g. .bashrc or .bash_profile:

PATH=$PATH:/home/john/jython export PATH

It is not necessary to run scripts by calling jython explicitly. To make your life simpler, put the following line as the very first line of your script:

#!/bin/env jython

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