box


SYNOPSIS

box  [mode={GET | SET; defaults to SET}]  \
    {[outgap=<number of Å by which the grid box exceeds the largest molecule in all directions; defaults to 5.0>]  \
    [step=<grid step size in Å; defaults to 1.0>]  \
    | [x_start=<top left x coordinate>  \
    {x_end=<bottom right x coordinate> | x_nodes=<number of nodes on the x coordinate>}  \
    y_start=<top left y coordinate>  \
    {y_end=<bottom right y coordinate> | y_nodes=<number of nodes on the y coordinate>}  \
    z_start=<top left z coordinate>  \
    {z_end=<bottom right z coordinate> | z_nodes=<number of nodes on the z coordinate>}  \
    | [file=<CoMFA .rgn file>]}


DESCRIPTION

The box keyword, whose default operation mode is SET, allows specifying the position, size and mesh of the grid box which surrounds the molecules belonging to the dataset. Before invoking box, some 3D structures must have been imported through the import type=SDF keyword. Invoking box without parameters creates a 1.0 Å step size box surrounding all molecules leaving a 5.0 Å outgap around the largest. Instead of specifying the grid box size through the outgap parameter, absolute x,y,z coordinates of the top left, bottom right corners may be given; the actual position of the bottom right corner will be adjusted to the nearest multiple of the grid step size. As an alternative to [x,y,z]_end parameters, the number of nodes on the x,y,z coordinates may be entered through the [x,y,z]_nodes parameters.
A grid box consistent with the one used in a CoMFA study may be created by importing a CoMFA region .rgn file through the file parameter.
Finally, invoking box with mode=GET outputs the current grid box settings.

EXAMPLES

# the following command creates a 1.0 Å step size box surrounding all molecules leaving a 5.0 Å outgap around the largest
box

# the following command creates a 0.3333 Å step size box surrounding all molecules leaving a 4.0 Å outgap around the largest
box  step=0.3333  outgap=4.0

# the following command creates a 1.0 Å step size box whose top left, bottom right corners have the following coordinates: [(21.0, 30.0, 27.0), (39.0, 46.0, 49.0)]
box  x_start=21.0  x_end=39.0  y_start=30.0  y_end=46.0  z_start=27.0  z_end=49.0

# the following command creates a 1.5 Å step size box whose top left corner has the following coordinates: (17.0, 21.0, 24.0); the number of nodes in the x, y, z directions are respectively 15, 18, 19
box  step=1.5  x_start=17.0  y_start=21.0  z_start=24.0  x_nodes=15  y_nodes=18  z_nodes=19

# the following command creates a grid consistent with the one used in a CoMFA study
box  file=comfa_study.rgn

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Last update:
May 31. 2015 20:39:55

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