Aligning the View to the Structure

There are occasions when you might want a particular view of a structure, along a bond in a molecule, or with a particular group in the plane of the screen, or along a particular crystal axis, for example. To set the view so that a particular structural feature is in a chosen orientation, choose View → Align View. A banner opens with various options for aligning the view to an axis or plane defined by atoms in a structure or by a periodic box.

To align the view to a structure:

1. For Align camera view to, select Structure.
2. Choose the camera view axis or plane from the Set option menu.
3. Pick atoms in the Workspace to define the axis or plane in the structure to which the camera view is to be aligned.
4. Click Align.

When the third atom is picked for a plane, a check is performed to ensure that the plane is uniquely defined (i.e. the atoms are not collinear). A blue-green plane is then displayed in the Workspace, and the Align button becomes available.

In addition to aligning the view, you can change the coordinates of the atoms in the structure, so that the coordinate system of the view becomes the coordinate system of the structure. To do this, click Update Coordinates.

To align the view to a crystal axis or plane:

1. For Align camera view to, select Box.
2. Choose the camera view axis or plane from the Set option menu.
3. From the To option menu, choose the axis or plane of the unit cell to which the camera view is to be aligned.
4. Click Align.

The x axis is the horizontal axis, the y axis is the vertical axis, and the z axis is the axis that projects out of the screen. The structure is rotated through the smallest possible angle to perform the alignment. If All axes is chosen for the alignment of the unit cell (which must be orthorhombic), more than one rotation is usually necessary to align all the axes.