8.8 Selection Tool

By this dialog box, you can select atoms, bonds, distances, angles, torsions and angles between two planes to perform a calculation. In 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, Bond, 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 step, 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 it in the main window.


Selection tool


To add the next atoms, repeat the atom selection.


Selection tool


To remove an atom, click 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 a whole selection, press Remove in the left box (Selections box) and to remove all selections at once, click New button.
The Open and Save buttons can be used to load and save the selections to 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.

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.