Box configuration file template

There are three methods for defining a custom 3D grid in pyKVFinder.

The first directly defines four vertices of the 3D grid (origin, X-axis, Y-axis and Z-axis), an example is shown below:

[box]
# px = [x, y, z]
p1 = [0.0, 0.0, 0.0]
p2 = [1.0, 0.0, 0.0]
p3 = [0.0, 1.0, 0.0]
p4 = [0.0, 0.0, 1.0]

Example: custom-box.toml.

The second defines a list of residues and a padding, the template is shown below:

[box]
residues = [ ["resnum", "chain", "resname",], ["resnum", "chain", "resname",], ]
padding =  3.5

Example: residues-box.toml.

The third uses parKVFinder’s TOML-formatted parameters file created by its PyMOL plugin.

[SETTINGS.visiblebox.p1]
x = 0.0
y = 0.0
z = 0.0

[SETTINGS.visiblebox.p2]
x = 1.0
y = 0.0
z = 0.0

[SETTINGS.visiblebox.p3]
x = 0.0
y = 1.0
z = 0.0

[SETTINGS.visiblebox.p4]
x = 0.0
y = 0.0
z = 1.0