View Grid Setup Parameter Block

Grid Center

enumerated choices: {Molecule Region|Picked Atom|Coordinates|Interfacial Region}

Choose how the grid region is to be defined. Each grid is defined by an absolute coordinate center, the grid size, and grid resolution. The options for the Grid Center parameter are: Molecule Region means that the region is defined by the coordinate limits of a molecule; Picked Atom means that the selected atoms coordinates define the center of the region; Coordinates means that the center of the region is an arbitrary point in cartesian space; Interfacial Region means that the intersection of two molecules define the region. This last definition is most useful for intertwined molecules such as protein subunits. The Border_Space is added to all sides of defined regions to get the final grid.

Molecule Region

identifier

This parameter, which is active if Grid Center is Molecule Extents or Interfacial Region, defines the molecule to be chosen for the definition. Choose a molecule or assembly object from the provided list. For Molecule Extents, the region will be defined as the size of the chosen molecule modified by the value of Border_Space.

Molecule Region 2

identifier

This parameter, which is only active if Grid Center is Interfacial Region, defines the molecule to be chosen for the definition. Choose a molecule or assembly object (different from the molecule to be chosen for the Molecule Region definition, above) from the provided list. The region will be defined as the intersection space of Molecule and Molecule2 modified by the value of Border_Space.

Atom at Center

identifier

This parameter, which is only active if Grid Center is Picked Atom, defines a specific atom to be the center of the Grid Space. The region will be modified by the value of Border_Space.

Center Coordinates

coordinate triplet

Enter the X, Y, and Z coordinates (in Angstroms) of an arbitrary point in space to be the center of the region. This coordinate point will be modified by the value of Border_Space to describe the map region.

Origin_On_Grid_Pt

on/off

The Origin_On_Grid_Pt parameter adjusts the center coordinates so that the real space origin (0.0, 0.0, 0.0) would lie exactly on a grid point if the grid were extended far enough in all directions. This is generally an unnecessary option, but may be required for interfacing to other display programs.

Grid Size

enumerated choices: {Border_Space|Total_Grid_Extent}

The Grid Size parameter defines the extent of the grid in Angstroms. The available options are:

Border_Space allows you to define a border to surround the region of the molecule defined by the Grid Center parameters. The specified Border_Space is added to both sides of each dimension (x,y,z) of the molecule or interface region to obtain the grid extents in each dimension.

Total_Grid_Extent allows direct specification of the Grid Size in the longest linear dimension of the molecule or interface. The Border_Space in this dimension is then calculated from the difference between the Total_Grid_Extent and the molecule bounds in this dimension, and this Border_Space is used for the other two dimensions.

Border Space

real number

Border_Space (in Angstroms) is subtracted from the minimum x, y, and z coordinates of the raw region, and added to the maximum x, y, and z coordinates of the raw region to define the final grid region.

Total Grid Extent

real number

The Total Grid Extent parameter defines the total distance (in Angstroms) the grid spans in the longest linear dimension. The grid extent in the other two dimensions is calculated to give the same border space as in the longest dimension.

Grid Resolution

enumerated choices: {Point_Spacing|Max_Grid_Points|Points_Per_Axis}

The Grid Resolution parameter allows you to specify the quantities which define the resolution of the grid. Since the extent of the grid is specified with the Grid Size parameters, the grid resolution is determined by the either the distance between grid points or the number of grid points along each axis. The available Grid Resolution options are:

Point_Spacing allows you to specify the actual resolution with the Angstroms/Grid Pt parameter. For most Hint calculations a spacing of 1.00 Angstrom is sufficient. Note that, unlike DelPhi which has special grid size and resolution considerations, Hint will accept any reasonable set of values. Thus, the Point_Spacing option is the most straightforward method of defining Grid Resolution and is the default.

Max_Grid_Points allows you to specify the number of grid points in the longest linear dimension (Max Points On Side). In this case, the point spacing is taken to be the total grid extent in the longest linear direction divided by the Max Points On Side.

Points_Per_Axis allows you to specify directly the number of grid points along each axis. The number of points and the total grid extent in the longest linear dimension are used to determine the point spacing. The other dimensions use the same point spacing, but may have different border spaces.

Angstroms/Grid Pt

real number

The Angstroms/Grid Pt is the spacing in Angstroms between adjacent grid points in all three directions.

Max Points on Side

integer number

The Max Points On Side parameter specifies the number of grid points in the longest linear dimension of the Hint grid. This value must be an odd integer greater than 3. For a given grid extent, the resolution and accuracy increases with increasing Max Points On Side, but the calculation time also increases.

X_Points

integer number

The X_Points parameter specifies the number of grid points along the x axis of the grid. This must be an odd integer greater than 3.

Y_Points

integer number

The Y_Points parameter specifies the number of grid points along the x axis of the grid. This must be an odd integer greater than 3.

Z_Points

integer number

The Z_Points parameter specifies the number of grid points along the x axis of the grid. This must be an odd integer greater than 3.