CrystalMaker Online Help

Toolbar Reference

Manipulation Tools

Rotate Tool lets you rotate an entire structure by clicking-and-dragging with the mouse

Move Tool allows you to drag the entire structure across the screen

Arrow Tool lets you:-

select or deselect atoms by clicking on them individually (shift-click for muliple atoms). This can be useful for defining a bond search (for a molecule), or for using the Edit > Hide Other Molecules command.
select groups of atoms by clicking on a blank area of the graphics window and, then dragging a selection rectangle over part of your structure;
move selected atoms, by clicking on one of them and dragging. Hold down the option key as you drag to duplicate the selection. To constrain movement horizontally or vertically, hold down the shift key as you drag.
select/deselect/move vectors (to edit vector settings, double-click on the vector tips with the arrow tool active)
move a text box or its associated line tip (to edit the text box settings, double-click on it with the arrow tool)

Rotate Selection Tool works like the Rotate Tool, except that only selected atoms are rotated; the rest of the structure remains fixed.

Selection Tools

Rectangle Tool lets you select atoms by clicking and dragging a selection rectangle over part of your structure.

Polygon Tool enables you to define a contiguous, irregularly-shaped selection. Click at successive points to define a closed path bounded by straight lines. To close the selection, click on your starting point again.

Lasso Tool lets you click and drag the mouse to define a freehand selection region.

Zapper Tool is a shortcut for hiding individual atoms or polyhedra. Click on an atom or polyhedron you wish to hide - you do not need to select them first. (Use the Selection > Show All command to recover hidden atoms.)

Measurement & Display Tools

Magnify Tool lets you zoom in or zoom out on a specific point in the structure. (Hold down the option or shift keys to zoom out.)

Info Tool lets you identify an atom or polyhedron by clicking on it. An info button allows you to summarize the site environment in the Output Window--or, by option-clicking on the info button, you can start a bond search around that particular site.

Text Tool lets you add or edit text boxes anywhere on the plot. Text boxes can contain multiple lines of text and may have lines or arrows from them.

Add/Delete Bond Tool lets you create a new bond, or destroy an existing bond between two atoms. Hold down the shift key as you click to generate similar bonds througout the entire structure.

Bond Distance Tool lets you measure the three-dimensional distance between a pair of atoms, or the centres of polyhedra. Click on two atoms and/or polyhedra with this tool, and the distance betwen them is displayed alongside. (Option-click the second atom to write the result to the Output window.)

Distance Tool provides a real-time measurement in the plane of the plot. Click once to anchor one end of the tool; the distance, in Angstrom units from the anchor to the mouse tip is displayed and updated as you move the mouse. Click a second time to freeze measurement.

Bond Angle Tool measures the included angle between three atoms. With this tool selected, click on three atoms or polyhedra, and their included angle is displayed alongside. (Option-click on the last atom to write the result to the Output window.)

Torsion Angle Tool lets you measure the torsion angle between four atoms. With this tool selected, click on four atoms A, B, C, and D. The torsion angle (i.e., angle between the vectors AB and CD) is displayed alongside.

Angle Tool lets you measure angles in the plane of the plot. Click at two points with this tool to anchor one line, then move the mouse to another point and click a third time. The included angle between two line segments is displayed alongside.

Lattice Plane Tool lets you display and move a lattice plane. With this tool selected you can click and drag a plane through a structure along the direction of its normal; you can rotate the plane by holding down the option key and dragging with the mouse.
Clicking again on the Lattice Plane Tool button displays the Show Lattice Plane dialog which allows you to adjust the plane's Miller indices (orientation), its colour, and its opacity.

Other Toolbar Buttons

Carousel Button (auto-rotation about screen Y axis)

Standard Size Button (graphics window is displayed on screen)

Fill Screen Mode (graphics window fills the entire screen, with its title bar hidden)

Auto-scale Button (replots the structure so that it fits snuggly within the graphics window for any orientation. Turns auto-scale mode on.

Auto-centre Button (centres the structure in the graphics window, leaving the scale/mode unchanged)

Zoom Out Button

Zoom In Button

Perspective Walk Backwards Button (For a perspective plot, reduces the plot scale and increases the view distance, giving the impression that one is moving further away from the structure.)

Perspective Walk Forwards Button (For a perspective plot, increases the plot scale and reduces the view distance, giving the impression that one is walking towards the structure.)

Main Menu

Manipulation Tools
	Rotate Tool lets you rotate an entire structure by clicking-and-dragging with the mouse
	Move Tool allows you to drag the entire structure across the screen
	Arrow Tool lets you:- select or deselect atoms by clicking on them individually (shift-click for muliple atoms). This can be useful for defining a bond search (for a molecule), or for using the Edit > Hide Other Molecules command. select groups of atoms by clicking on a blank area of the graphics window and, then dragging a selection rectangle over part of your structure; move selected atoms, by clicking on one of them and dragging. Hold down the option key as you drag to duplicate the selection. To constrain movement horizontally or vertically, hold down the shift key as you drag. select/deselect/move vectors (to edit vector settings, double-click on the vector tips with the arrow tool active) move a text box or its associated line tip (to edit the text box settings, double-click on it with the arrow tool)
	Rotate Selection Tool works like the Rotate Tool, except that only selected atoms are rotated; the rest of the structure remains fixed.

Selection Tools
	Rectangle Tool lets you select atoms by clicking and dragging a selection rectangle over part of your structure.
	Polygon Tool enables you to define a contiguous, irregularly-shaped selection. Click at successive points to define a closed path bounded by straight lines. To close the selection, click on your starting point again.
	Lasso Tool lets you click and drag the mouse to define a freehand selection region.
	Zapper Tool is a shortcut for hiding individual atoms or polyhedra. Click on an atom or polyhedron you wish to hide - you do not need to select them first. (Use the Selection > Show All command to recover hidden atoms.)

Measurement & Display Tools
	Magnify Tool lets you zoom in or zoom out on a specific point in the structure. (Hold down the option or shift keys to zoom out.)
	Info Tool lets you identify an atom or polyhedron by clicking on it. An info button allows you to summarize the site environment in the Output Window--or, by option-clicking on the info button, you can start a bond search around that particular site.
	Text Tool lets you add or edit text boxes anywhere on the plot. Text boxes can contain multiple lines of text and may have lines or arrows from them.
	Add/Delete Bond Tool lets you create a new bond, or destroy an existing bond between two atoms. Hold down the shift key as you click to generate similar bonds througout the entire structure.
	Bond Distance Tool lets you measure the three-dimensional distance between a pair of atoms, or the centres of polyhedra. Click on two atoms and/or polyhedra with this tool, and the distance betwen them is displayed alongside. (Option-click the second atom to write the result to the Output window.)
	Distance Tool provides a real-time measurement in the plane of the plot. Click once to anchor one end of the tool; the distance, in Angstrom units from the anchor to the mouse tip is displayed and updated as you move the mouse. Click a second time to freeze measurement.
	Bond Angle Tool measures the included angle between three atoms. With this tool selected, click on three atoms or polyhedra, and their included angle is displayed alongside. (Option-click on the last atom to write the result to the Output window.)
	Torsion Angle Tool lets you measure the torsion angle between four atoms. With this tool selected, click on four atoms A, B, C, and D. The torsion angle (i.e., angle between the vectors AB and CD) is displayed alongside.
	Angle Tool lets you measure angles in the plane of the plot. Click at two points with this tool to anchor one line, then move the mouse to another point and click a third time. The included angle between two line segments is displayed alongside.
	Lattice Plane Tool lets you display and move a lattice plane. With this tool selected you can click and drag a plane through a structure along the direction of its normal; you can rotate the plane by holding down the option key and dragging with the mouse. Clicking again on the Lattice Plane Tool button displays the Show Lattice Plane dialog which allows you to adjust the plane's Miller indices (orientation), its colour, and its opacity.

Other Toolbar Buttons
	Carousel Button (auto-rotation about screen Y axis)
	Standard Size Button (graphics window is displayed on screen)
	Fill Screen Mode (graphics window fills the entire screen, with its title bar hidden)
	Auto-scale Button (replots the structure so that it fits snuggly within the graphics window for any orientation. Turns auto-scale mode on.
	Auto-centre Button (centres the structure in the graphics window, leaving the scale/mode unchanged)
	Zoom Out Button
	Zoom In Button
	Perspective Walk Backwards Button (For a perspective plot, reduces the plot scale and increases the view distance, giving the impression that one is moving further away from the structure.)
	Perspective Walk Forwards Button (For a perspective plot, increases the plot scale and reduces the view distance, giving the impression that one is walking towards the structure.)