Viewing your molecule

Molecule style: Balls and Sticks, Sticks, or Wireframe

The molecule style can be selected via the View menu (View → Molecule → …). You can select Balls and Sticks, Sticks, Wireframe or Hidden. This choice will affect the whole molecule. Note that if you use anything else then Balls and Sticks it will become much more difficult to select an atom (as there is no ball representing it).

You can also use different styles at the same time, for different regions. To do that, go to the Regions panel, make regions as you like, and set the molecule style from the pop-up menu per region in the Regions panel (the downward pointing triangle at the end of each region line).

Multiple views

Use View → Multiple Views to split the molecule window into three synchronized views. This is useful when you want to inspect the same structure from several directions at the same time.

You can drag the divider between the main view and the two smaller views to adjust their relative sizes. The layout is saved per GUI module.

You can also double-click the divider to restore the default layout.

Use View → Multiple View Settings → Reset Multiple View Layout to restore the default layout.

For periodic systems, View → Multiple View Settings → Multiple View Basis lets you choose whether the three views use the Cartesian axes or the periodic directions.

Camera position: view direction

You can use the mouse to view your molecule from a different position.

In some situations you may want to view your molecule from some very specific angle. Use View → View Direction for this. The following commands are always available:

  • View → View Direction → Along X-axis

  • View → View Direction → Along Y-axis

  • View → View Direction → Along Z-axis

For periodic systems, extra commands are available to look along the periodic directions:

  • View → View Direction → Along a-axis

  • View → View Direction → Along b-axis

  • View → View Direction → Along c-axis

Here, a, b, and c refer to the lattice vectors of the periodic system.

The exact periodic options depend on the dimensionality of the system:

  • For a 1D periodic system, only Along a-axis is available.

  • For a 2D periodic system, the third periodic command is shown as Along a×b-axis. This looks along the direction normal to the periodic plane.

  • For a 3D periodic system, Along a-axis, Along b-axis, and Along c-axis are available.

For non-periodic systems, three extra commands are available:

  • View → View Direction → Along Principal Axis 1

  • View → View Direction → Along Principal Axis 2

  • View → View Direction → Along Principal Axis 3

These three directions are the principal axes of inertia of the current structure, ordered by increasing principal moment of inertia.

Keyboard shortcuts

Use ⌘-1, ⌘-2, and ⌘-3 on macOS, or Ctrl-1, Ctrl-2, and Ctrl-3 on other systems, to look along the X-, Y-, and Z-axis.

Use ⌘-4, ⌘-5, and ⌘-6 on macOS, or Ctrl-4, Ctrl-5, and Ctrl-6 on other systems, for the extra direction commands. For periodic systems these shortcuts select the crystal directions a, b, and c (or the direction normal to the ab plane for the third direction in a 2D periodic system). For non-periodic systems the same shortcuts select Principal Axis 1, 2, and 3.

View direction in multiple views

If View → Multiple Views is enabled, the selected direction is applied to the current view and the other views are updated automatically to remain orthogonal.

If View → Multiple View Settings → Multiple View Basis → Periodic is used for a 2D periodic system, the three views correspond to the a lattice vector, the b lattice vector, and the direction normal to the periodic plane. Selecting one of these directions makes that direction the active view. The other two views show the remaining two directions, so the three panes continue to show the full periodic basis without duplication.

Align Screen

Using this command, you can align the screen parallel to some plane in your molecule. You need to select three atoms first which will define the plane to align to.

Camera positions

First view your molecule from your favorite position (or use one of the just mentioned commands). Next, you can store the camera position by selecting one of the Save 1-5 commands. That will store the current view in the selected slot. To switch to one of the stored views, use one of the Load 1-5 commands.

The camera positions are saved for all GUI modules to use. Thus, if you start AMSinput (or any other GUI module with a View menu) the stored camera positions are available everywhere. This makes it possible to force the use of the same camera position in different GUI modules.

The Camera menu can be torn off, which is very convenient if you have several views that you wish to switch between frequently. To tear off the menu, select the dashed line in the Camera menu.

3D

The GUI modules do have support for real 3D viewing. Use the View → 3D menu to select what kind of stereoscopic display you have. The simplest version is having none, but using colored glasses (like the Red-Cyan). The other options are for special hardware. Just try out what works for you. This is a rather new and not completely stable feature, so it may not work for you.

One known but at the moment this is written unsolved problem is that the 3D view does not work on Mac OS X using Lion (it does work with Snow Leopard).

Fly to selection

When you have a big system, it often make sense to zoom in to some particular region. To do this, use the View → Fly To Selection menu command.

Not only will this zoom in to the selected atoms, but the center of the selected atoms will also become the new center of rotation when you use the mouse to get a different view.

Reset View

You can reset the view using the View → Reset View menu command. This is especially useful after flying to the selection. Or when the view gets distorted for some reason.