User guide

1. To display the Query tools, go to View>Other Toolbars>Query Tools or click the Query Tools icon on the Main
Tool palette.
2. On the Query tools palette, click the tool for the flag you want to use.
3. Click next to the structure to which you want to assign the flag.
3D properties
3D queries are useful in pharmacophore searching when looking for a 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 can 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:
1. Select the structure or substructure.
Note: Because some 3D properties specify an order, use SHIFT+Click to select them in the order you want.
2. Go to Structure>Add 3D Property and select an option from the table below.
Note: In the table, points may be atoms, centroids or points. Lines may be lines or normals.
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 angstroms, 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.
When you create a point, a dialog box appears. Specify the distance from the first selected point to the calculated
point. The distance may be an absolute value in Å or a percentage of the distance between the selected points. Neg-
ative values indicate that the calculated point is further from the second point than the first point is, rather than
between them.
ChemBioDraw 13.0
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