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Installation of the surfrace program for the calculation of accessible surface areas and curvatures.


update 04/2013: The SurfaceRacer wrapper has been updated in the svn trunk to work with v 5.0 of the program. The original update from Sept. 2013 had introduced a regression bug. Please use revision 1137 or later.
  1. Download Surface Racer 5.0 from and unpack the file into a temporary folder, e.g:

    cd /tmp
  2. Test that the binary works. Run the program from within it's unpacked folder:

    cd /tmp/surface_racer_5.0_64bit
    chmod +x surfrace5_0_linux_64bit

    Should yield:

    Surface Racer 5.0 by Oleg Tsodikov
    Analytical surface area calculation

    And will then ask you for input files.


    If you get the following error:

    ./surfrace5_0_linux_64bit: error while loading shared libraries:
    cannot open shared object file: No such file or directory

    You will have to install version 5 of the GNU standard C library (default is currently 6.0). This older version can co-exist with the current version. On Ubuntu:

    sudo apt-get install libstdc++5
  3. Copy the executable into some more standard location, e.g.:

    sudo cp surfrace5_0_linux_64bit /usr/local/bin/surfrace
    sudo chmod +x /usr/local/bin/surfrace

    (or keep the same executable name but set a symbolic link to 'surfrace'). If you are using a different executable name or a location that is not in your $PATH, you need to configure .biskit/exe_surfaceracer.dat. See below!

  4. Test your installation by running

    cd ~/biskit
    python Biskit/

    should yield:

    Loading PDB...
    Starting SurfaceRacer
    Running (adding SurfaceRacer to local namespace as x)
    Curvature: weighted mean -0.047307 and standard deviation 0.209
    Relative MS of atoms 10 to 20 atoms: [   0.           74.7911711

Use Surface Racer in non-standard location

if you are using a different executable name or a location that is not in your $PATH, you need to tell biskit about the new location:

  1. Create a custom copy of the SurfaceRacer configuration file:

    cd ~/.biskit/
    cp ~/biskit/Biskit/data/defaults/exe_surfaceracer.dat .
  2. Adapt the field bin=, e.g.:

    ## binary
  3. Save the file and test as before.

Note for using surface racer stand-alone

Surface racer needs to be executed in the same directory where both the input PDB and the radii.txt file are located. creates a temporary folder on the fly into which it links all the necessary files, then collects the result and removes the folder again.

If you want to use Surface Racer stand-alone, you need to copy the folder contained in the zip file to some (writable) location and copy your pdb file into it. Biskit uses a copy of the radii.txt file which is checked into biskit/external/surface_racer_3/. That's why the naked executable is enough.

see PDBDope.addSurfaceRacer()
Custom configuration:
see biskit/Biskit/data/defaults/exe_surfaceracer.dat