5.10 Grid Visualization

Grids are spatial arrays of data that are sampled at regular intervals. Grids may contain electrostatic samples of spatial regions, density samples, and other potential fields.

A grid can have a variable number of contours. Each contour has an index starting at 1 for the first contour. Additionally, every contour has its own individual color and a threshold value which can be positive or negative (also known as the ``contour level"). There are three different display styles for grids contours: Solid, Mesh and Cloud.

5.10.1 Grid Types

As mentioned in the previous section, there are multiple different predefined grid types that are supported including: Electrostatic, ET, FRED, Generic, Difference Map, and Regular Map.

5.10.1.1 Electrostatic

Electrostatic grids are the only type of grid that can be actually be generated within VIDA as opposed to simply being visualized. Electrostatic grids are created for individual molecules using OpenEye's Zap toolkit. The creation of the grid requires the presence of partial charges on the input molecule. If partial charges were already present on the molecule, those will be used in the calculation. However, if no partial charges were present (or the user decides to ignore them, which can be done in the application preferences), temporary partial charges will be calculated using MMFF94 or AM1-BCC [3,4]. If a molecule has greater than 50 atoms, MMFF94 charging will be done even if AM1-BCC was selected. However, for proteins an alternate residue based charging model is available and can be selected in the preferences. This model assigns partial charges based on residue information as is shown below:

ASP	OD1, OD2	-0.5
GLU	OE1, OE2	-0.5
LYS	NZ	+1.0
ARG	NE	+1.0
Other		0.0

The grid resolution is dynamically determined based on the number of atoms in the input molecule. However, it is possible to specify a fixed resolution in the grid preferences. Be warned, however, that specifying very fine resolutions (<2.0 Angstroms) may consume a surprisingly large amount of memory, and in some cases more than may be available on the computer, which can lead to program failure. This should be consider a very advanced feature to be used only when necessary and when all other data has been saved. Finally, it has been observed in research at OpenEye that adding salt to the electrostatic calculation has a good effect on the grids generated. The salt concentration can be specified in the preferences. The default concentration is 0.04 M. The maximum concentration that can be specified is 0.1 M.

Electrostatic grids (as well as ET grids) are special in that they are always generated with two default contours: a positive one and a negative one. These contours cannot be deleted and new contours cannot be added. The positive contour is colored blue by default and the negative contour is colored red. The contour levels of the two contours are coupled together and so changing one will change the other.

5.10.1.2 ET

ET (or Electrostatic Tanimoto) grids are generated by OpenEye's Brood and EON applications. When viewed in VIDA, they behave and are treated essentially the same as Electrostatic grids (see Section 5.10.1).

5.10.1.3 FRED

FRED grids are shape potential grids that are created by OpenEye's FRED application. In VIDA, the behave just like Generic grids (see Section 5.10.1) except that their default contour color is purple instead of blue.

5.10.1.4 Generic

Generic grids are effectively the most basic grids and act as the primary grid workhorses. They are completely customizable and have bare-bones settings. They default to having just one contour with a default color of blue. Additional contours can be added as well as removed. These default values can be changed in the Grids section of the application preferences.

5.10.2 Reentrant Grids

**Figure 5.18:** Grid contouring examples showing (a) an infinite grid (b) the same grid rendered at a different center, notice that the grid is rendered in the center of the scene, not at the molecule and (c) a finite density grid showing the grid corners or extent of the grid.
[Reentrant] [Reentrant] [Non-reentrant]

Some grids have fixed extents and some grids are infinitely reentrant in space. Reentrant grids obviously cannot be displayed in their entirety, so instead only the region around the center of the current scene is displayed. Grids that are being rendered as reentrant can be distinguished from non-reentrant grids by the absence of grid corners which define the extents of non-reentrant grids.

				VIDA User Manual

				VIDA User Manual