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Install the TM-Align structure alignment program (Zhang and Skolnick 2003).

Program binaries for 64 and 32 bit Linux are provided on the TM-Align home page:

Later versions of TMalign (since 2012) have changed output formats. The Biskit wrapper has been adapted to TMAlign.f (Fortran version) as downloaded from the Zhang lab website 04/2013.
  1. Download and uncompress the file and make it executable:

    cd /tmp
    gzip -d TMalign.gz
    chmod +x TMalign
  2. Copy it to a system-wide location:

    sudo mv TMalign /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_tmalign.dat configuration file and adapt it accordingly:

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

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

  4. Test your installation:

    cd biskit/Biskit/

    Should yield:

    <....some example data ....>
    Ran 2 tests in 4.238s

  • see Biskit.TMAlign
  • see Biskit.PDBModel.structureFit()
see Biskit/data/defaults/exe_tmalign.dat