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SurfaceRacer

Installation of the surfrace program for the calculation of accessible surface areas and curvatures.
  1. Download Surface Racer 5.0 from http://pharmacy.uky.edu/research-innovation-and-discovery/faculty-labs/tsodikov-laboratory/software and unpack the file into a temporary folder, e.g:

    cd /tmp
    wget http://pharmacy.uky.edu/research-innovation-and-discovery/\
         faculty-labs/tsodikov-laboratory/software/surface_racer_5.0_linux64.zip
    unzip surface_racer_5.0_linux64.zip
    
  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
    ./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.

    Troubleshooting:

    If you get the following error:

    ./surfrace5_0_linux_64bit: error while loading shared libraries: libstdc++.so.5:
    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 Biskit.SurfaceRacer.py:

    cd ~/biskit
    python biskit/exe/surfaceRacer.py
    

    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
    bin=/cluster/shared/bin/surfrace
    
  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. Biskit.SurfaceRacer.py 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.


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