Nanoparticle Builder — Alignment Options Dialog Box

Align the nanoparticle boundaries automatically to crystal faces and edges, or manually by translating and rotating the shape template in the Workspace.

To open this dialog box, click Alignment Options in the Nanoparticle Builder Panel.

  • Using
  • Features
  • Additional Resources

Using the Alignment Options Dialog Box

By default, the template shape for the nanoparticle is centered at the origin and aligned to the coordinate axes. If this is not the position and alignment you want, you can use the tools in this dialog box to place and orient the template shape where you want it. There are two sets of tools for positioning and aligning the template shape.

Automatic alignment to specified directions and location
These tools allow you to align a chosen face of the template shape to a plane, align the edge of that face to another normal vector, and move the origin of the shape to a specified set of coordinates. The position and orientation of the template shape is updated in the Workspace as you make these changes.

Manual alignment
You can manually align the template shape with the Maestro actions you use for translating and rotating a structure.

Alignment Options Dialog Box Features

Face alignment options

Align the normal to the selected face along a chosen vector. The choices for the face depend on the shape you chose for the nanoparticle in the Nanoparticle Builder panel. The vector can be defined in reciprocal space (hkl), in terms of the unit cell vectors (abc), or in real space (xyz). You can set the values for each of the three vector components in the text boxes. The alignment of the template in the Workspace is adjusted as you make changes to these options.

Edge alignment options

With the current face alignment, align the selected edge of that face along a chosen vector, by rotating the template shape. The choices for the edge depend on the shape you chose for the nanoparticle in the Nanoparticle Builder panel. The vector can be defined in reciprocal space (hkl), in terms of the unit cell vectors (abc), or in real space (xyz). You can set the values for each of the three vector components in the text boxes. If this vector is not orthogonal to the face normal, its orthogonal component is used for the edge alignment. The alignment of the template in the Workspace is adjusted as you make changes to these options.

Origin options

Set the origin of the cluster. You can set it to the centroid of all atoms in the Workspace or the selected atoms in the Workspace by clicking one of the buttons, or to a particular set of (x,y,z) coordinates by entering values in the text boxes. Clicking the buttons sets the values in the text boxes, which can then be changed. The values in the text boxes are the values actually used for the centroid. The alignment of the template in the Workspace is adjusted as you make changes to these options.

Manual alignment option

Position and orient the template shape in the Workspace by using the Workspace translation and rotation mouse actions.

Rotate and translate the template shape option

Apply the rotation and translation actions to the template shape, rather than to the entire Workspace (changing the view of the Workspace). To change the view when this option is selected, you can hold down the SPACEBAR while you move the mouse.

Include face and edge alignment unit vectors in shape template option

Display arrows that indicate the vectors used for the face and edge alignments.

Reset button

Reset all options and values to their default values.

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