SurfaceRacer

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

Download Surface Racer 5.0 from https://tsodikovlab.createuky.net/index_files/Surface_Racer.htm and unpack the file into a temporary folder, e.g:
```
cd /tmp
wget https://tsodikovlab.createuky.net/files/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

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

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/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:

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.

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

Personal tools

SurfaceRacer

Use Surface Racer in non-standard location

Note for using surface racer stand-alone