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.
Download Surface Racer 5.0 from http://pharmacy.mc.uky.edu/faculty/tsodikov/software.php and unpack the file into a temporary folder, e.g:
cd /tmp wget http://pharmacy.uky.edu/sites/pharmacy.uky.edu/files/files/tsodikov/surface_racer_5.0_linux64.zip unzip surface_racer_5.0_linux64.zip
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
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: 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
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!
Test your installation by running Biskit.SurfaceRacer.py:
cd ~/biskit python Biskit/SurfaceRacer.py
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:
Create a custom copy of the SurfaceRacer configuration file:
cd ~/.biskit/ cp ~/biskit/Biskit/data/defaults/exe_surfaceracer.dat .
Adapt the field bin=, e.g.:
## binary bin=/cluster/shared/bin/surfrace
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.
- see PDBDope.addSurfaceRacer()
- Custom configuration:
- see biskit/Biskit/data/defaults/exe_surfaceracer.dat