HOLLOW

in the IDLE interpreter

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:

  1. Copy your pdb files to the same directory as the hollow.py file

  2. 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

  3. Now click on the window that shows the Hollow.py file.

  4. 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.

  5. In the Python Shell Window type:

    >>> import hollow

  6. If you need to see the message again:

    >>> hollow.help()

  7. 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)

    >>> hollow.make_hollow_spheres('3HBS.pdb')


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

Once the hollow spheres are generated, you can generate surfaces for channels or interior voids.