Selections And restraints
When you've selected a group of atoms, you have the option to save this selection for future reference. To do this, simply choose the group of atoms you're interested in, then go to the 'Selections' menu in the main toolbar and select 'Add to Selection List.' You can review the list of selected atoms for each system in the 'Selection and Restraints' window, accessible through the toolbar in the main window (see Figure 1).
Figure 1: The auxiliary window allows the user to access the lists of selected atoms. To activate a selection, simply double-click with button one on the desired item in the treeview. The numbers 1, 2, and 3 indicate fixed atoms, atoms from the QC region, and a selection of atoms added to the list, respectively. The list of atoms in the QC region and fixed atoms automatically appears in the list by default.
When the user wants to activate one of the lists of selected atoms, it is important for them to specify the system and the set of coordinates in which the selection should be applied. This can be done using the 'System' and 'Coordinates' comboboxes located at the top of the window.