Selecting¶

In many modules there are menu commands to select atoms:

Select All: select all atoms in your system.
Invert Selection: all atoms in your system currently not selected will be the new selection.
Select Molecule: extent the current selection so that all atoms connected (by bonds as visible) to it are included in the selection.
Select Connected: extent the current selection so that all atoms directly connected (by bonds as visible) to it are included in the selection. Thus repeated use of this command will select all atoms in your molecule (same as Select Molecule).
Select Atom Close To Origin: select one atom close to the origin. Often useful to select one atom in a crystal, and next selecting atoms in a sphere around it (with the next command).
Select Within Radius: set the selection to all atoms in a sphere with specified radius around the center of the current selection.
Make Selection Cappable: extent the current selection such that it is acceptable as a region for the Hybrid engine, were all bonds to other parts will be capped. A cappable region should not have bonds with an order > 1.25 to atoms not in the region, and atoms outside the region should have at most one bond to atoms inside the region. This command will extent the selection so that these requirements are handled.
Select Atoms Of Same Type / PDBName: extent the selection with atoms with the same Type (element) or PDBName.

Selecting regions from results¶

If a result file contains region definitions, you can select their atoms in the molecule view. Open Select Region from the menu listed below, then choose a region name.

Table 1 Region selection in result viewers¶
GUI module	Menu
AMSview	Select → Select Region
AMSmovie	Select → Select Region
AMSdos	Edit → Select Region
AMSbandstructure	View → Select Region
ParAMS	View → Select Region
AMSspectra: vibration, Raman, and PVDOS	Select → Select Region
AMSspectra: NMR and VCD	Regions → Select Region

Choosing a region replaces the current atom selection with all atoms in that region. Atoms can belong to more than one region. When regions are available, All selects all atoms in the active molecule.

The menu shows the regions of the active molecule. Open it again after switching result files, molecules, or trajectory frames to see the current regions. If the molecule has no region definitions, the menu shows a disabled No regions available entry.

In AMSbandstructure, choose a region name in View → Select Region to select its atoms and switch the 3D view from the Brillouin zone to the atoms. The Atoms control below the 3D view also switches to the atom display. In ParAMS, use View → Molecule Window to show the molecule if its display is hidden.

In AMSbandstructure, select atoms or a region, then choose a projection from the Bands or DOS menu. Total and orbital projections, dominant-character coloring, and cumulative DOS use the selected atoms. Clear the selection before choosing a projection to use all atoms. Each choice keeps the atoms selected at that time; changing the selection does not change an existing plot.