model.make_region() -- define a random surface patch of atoms

atom_accessibility = <float:1>	1.0	accessible atoms for MAKE_REGION
region_size = <int:1>	20	size of exposed region in MAKE_REGION

Description:

This command defines a contiguous patch of exposed atoms of the specified size. First, the exposed atoms in MODEL are identified by using the atom_accessibility cutoff (in $\mbox{\AA}^2$). The seed atom is picked randomly among the exposed atoms. The patch is expanded by iteratively adding the exposed atom that is closest to the gravity center of the currently selected patch atoms. Thus, the patch is defined deterministically once the seed atom is picked. The patch is defined by setting the fourth column parameter ($B_{iso}$) to 1 for the patch atoms and to 0 for the remaining atoms. The ``temperature'' color option of Rasmol can be used to display the patch graphically.

To obtain surface patches that look good in visual inspection, it is necessary to use a non-obvious scaling factor for atomic radii and probe radius for solvent calculation by model.write_data(), as well as the accessibility cutoff for model.make_region().

Example: examples/commands/make_region.py

# Example for: model.make_region()

# This will define a random contiguous patch of atoms on a surface of the
# protein.

env = environ(rand_seed=-18343)
log.level(1, 1, 1, 1, 0)

# Read the PDB file
mdl = model(env)
mdl.read(file='../atom_files/pdb1fdn.ent')

# Calculate atomic accessibilities with appropriate probe_radius
mdl.write_data(output='PSA ATOMIC_SOL', psa_integration_step=0.05,
               probe_radius=0.1)

# Get the "random" patch of exposed atoms on the surface
mdl.make_region(atom_accessibility=0.5, region_size=35)

# Write out a PDB file with the patch indicated by Biso = 1:
mdl.write(file='1fdn.reg')