Although HOLLOW was designed to be a command-line utility running under a UNIX environment, it can also be used in the PYTHON interpreter. This is useful in WINDOWS, for instance, which is not very friendly to command-line utilities.
To use HOLLOW in the Python interpreter:
Copy your pdb files to the same directory as the hollow.py file
Assuming that Python is installed properly, to launch HOLLOW in the IDLE Python interpreter, go to your file manager and double click on hollow.py. Otherwise, right-click and choose:
Edit with IDLE
Now click on the window that shows the Hollow.py file.
Go to the pull-down menu and choose Run->Run Module, which will take you to the Python Shell Window. This should print out a help message.
In the Python Shell Window type:
>>> import hollow
If you need to see the message again:
The definition of the python routine that carries out the HOLLOW calculation is:
make_hollow_spheres( pdb, out_pdb="", grid_spacing=0.5, size_interior_probe=1.4, is_skip_waters=True, size_surface_probe=8.0 constraint_file="", size_bfactor_probe=0)
Let's say you are studying the PDB file 3HBS.pdb, the following commands can be used to run HOLLOW using different options:
>>> hollow.make_hollow_spheres('3HBS.pdb','hollow.pdb', 0.5)
>>> hollow.make_hollow_spheres('3HBS.pdb', 'hollow.pdb', 0.5,1.40,True,8.00,'2oi2.constraint',4.0)
>>> hollow.make_hollow_spheres('3HBS.pdb', grid_spacing=0.25)
The output of the program should look something like this:
Loading 3BHS.pdb Skipping water molecules Setting up grid: 233 x 233 x 233, spacing 0.500, width 116.9 >>>>>> 11.21s Excluding protein bulk from grid with 1.4 angstrom probe >>>>>> 15.62s Calculating asa of atoms in protein >>>>>> 2:38.55s Excluding surface shell from grid with 8.0 angstrom probe >>>>>> 14:25.54s Excluding edges Excluding surrounded points >>>>>> 58.66s Saving hollow spheres to 3BHS-hollow.pdb