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Reduce

Install the Reduce program for adding of hydrogens to proteins and nucleic acids (Word et al. 1999)

Note (2016): Reduce is now included in the AmberTools package (v.15). There is no need to install it separately.

Program binaries for Linux, Mac and Windows as well as the full source package are provided at the Reduce home page: http://kinemage.biochem.duke.edu/software/reduce.php

  1. Download and uncompress the file and make it executable:

    cd /tmp
wget "http://kinemage.biochem.duke.edu/php/downlode.php?filename=\
/downloads/software/reduce31/reduce.3.23.130521.linuxi386.gz"
mv downlode*gz reduce.gz
gzip -d reduce.gz
chmod +x reduce

  2. Copy it to a system-wide location:

    sudo mv reduce /usr/local/bin/

    ...or any other location that is in your search $PATH. As always, you can also configure Biskit to find the program somewhere else:

  3. Adapt biskit settings (optional):

    This would only be necessary if the executable has a different name or is not in the search $PATH. Make a local copy of the exe_reduce.dat configuration file and adapt it accordingly:

    cd /usr/lib/python2.5/site-packages/Biskit/data/defaults
cp exe_reduce.dat ~/.biskit/

    Then edit the "bin=" line in the [BINARY] section of this file.

  4. Test your installation:

    cd biskit/Biskit/
python reduce.py

    Should yield:

    <....some example data ....>
---------------------------------------
Ran 1 test in 1.238s

OK
Usage:
  • see Biskit.Reduce
Configuration:
see Biskit/data/defaults/exe_reduce.dat