3D Properties

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3D queries are particularly useful in pharmacophore searching where the user is looking for a particular 3D relationship among atoms and bonds, for example in a series of potential receptor ligands. To create a 3D query, you add geometries (lines, planes, etc.) and constraints (specified as ranges) to a query structure. For example, you might specify that two atoms must be between 4 and 5 Å apart, or that two planes must be separated by 80-100 degrees.

To assign 3D properties to a structure, select the structure or sub-structure and then select one of the following options from the Add 3D Property entry on the Structure menu.

NOTE: Because some 3D properties specify an order, you should use Shift+Click to select them in the proper order rather than using the Marquee or Lasso tool to select them all at once.

In the table below, points are may be atoms, centroids or points. Lines may be lines or Normals.

Option	Search Result
Angle	Defines an angle constraint between three points (in order). Indicated as a range.
Dihedral	Defines a dihedral (torsional) angle constraint among four points (in order), between two lines, or two planes. Indicated as a range.
Distance	Defines a distance constraint between two points, a point and a line, or a point and a plane. Indicated as a range, in Angstroms.
Line	Defines the best-fit line for the selected points.
Plane	Defines the best-fit plane for the selected points, or for a point and a line.
Exclusion Sphere	Defines an exclusion sphere around a point. If more than one point is selected, the exclusion sphere is around the first selected point, and the subsequent points are allowed within the exclusion sphere when the query is evaluated. Indicated as a range, in Å, beginning at 0.
Normal	Defines the normal from a defined plane in the direction of a point.
Point	Defines a point positioned at a specified distance from a first point in the direction of a second point (in order), or in the direction of the normal.
Centroid	Defines a point positioned at the average position of all other points selected.

All constraint values can be edited with the text tool. Only exclusion spheres show the change visually.

When you create a point, a dialog box is displayed. Specify the distance from the first selected point to the calculated point. The distance may be specified as an absolute value in Å or as a percentage of the distance between the selected points. Negative values indicate that the calculated point is further from the second point than the first point is, rather than being between them.

Geometry and constraint objects update dynamically when you change the structure; they cannot be moved independently. They may be used with .cdx, .mol, .skc, and .tgf files (full read-write compatibility); they are not compatible with other formats. They can, however, be saved in print-only formats such as TIFF.