8.8 Selection Tool

With this dialog box, you can select atoms, distances, angles, torsions and angles between two planes to perform a calculation. In the Selection Tool,  you can compile the atom list using the atom name, residue name, residue number format or the simple atom number.
As first step, choose the selection type (Distance, Angle, Torsion, Plane Angle, Multiple). The Multiple selection is needed if you want select one or more atoms without a geometric relation and it will be useful in the next VEGA ZZ releases.

Selection tool

At this point, press Add and automatically a default name will be shown. If you want rename it, just type in Name field.

New distance

Select the first atom clicking on it in the main window.

To add the next atoms, repeat the atom selection.

To remove an atom, click on the atom in the list and press Remove in the right box. To change the order of atoms in the list, use the Up and Down buttons. To remove an entire selection, press Remove in the left box (Selections box) and to remove all selections at once, click the New button.
The Open and Save buttons can be used to load and save the selections into a .sel file. For more information about this file format, click here.

Context menu

The context and Edit menus allow to add automatically torsions:

Menu item Submenu Description
Add torsions All Add all possible torsions.
AutoDock Add the torsions needed by AutoDock to perform the in situ conformational search.
Flexible

Add the flexible torsions only. This feature is very useful to perform a conformational search.

Add protein torsions Omega Add omega torsions.
Phi Add phi torsions.
Psi Add psi torsions.

To remove all selections, select Remove all in the Edit menu.. When the selection is finish, you must click the Done button or select the File -> Close menu item to close the dialog window.