Atom->Select is used for two different things: 1) to set an
atom as the current object (the object that is moved, rotated, scaled
with the mouse); 2) to select a whole list of atoms that can be
subsequently modified or removed using Atom->Modify or Atom->Remove.
To set an atom as the current object, click the mouse over its
visual representation. When an atom is recognized, a beep is emitted
and the atom identification is shown in the window status bar, first
in a highlighted color (to emphasize that the current object has
changed) and then in the default color (after a few seconds).
Only atoms in the working layer can be chosen as current object,
even if atoms are visible in other (transparent or translucid)
layers. For each top window, only one current object is maintained.
This can be Gamgi (everything), Window (the current window),
Layer (the current layer), or a child object of the current
layer. The identification of the current object is always
visible in the window statusbar.
A faster method to set an atom as current object,
without using the Atom->Select dialog, is to click over
Atom on the main menu with the second mouse button,
and then click over the atom visual representation.
List
List always shows a flat list of all the atoms available
in the current 
Scope. For each atom, a hierarchical tree
shows all its child objects.
Scope
This sets the initial 
List of candidate atoms, presented
on the left, from where the atoms will be selected. Five options
are available: 
Gamgi (atoms in all windows), 
Window
(atoms in the current window), 
Layer (atoms ins the current
layer), 
Before (the previous list of selected atoms) and
Current (the current list of selected atoms).
The list 
Before allows users to undo possible mistakes
and is removed everytime Atom->Select closes. The list
Current is the real thing, the list of atoms that
is saved for further action when Atom->Select is closed.
When list 
Current is not empty, the 
Atom label
on the main menu shows a different color, to signal that a
list of atoms has been selected.
By default GAMGI always shows the list 
Current, except when
this list is empty (for example the first time 
Atom->Select
is called). In this case GAMGI starts with the list 
Layer.
Thus the new list 
Current is usually prepared selecting
objects from the existing list 
Current. This gives users a
simple and effective way to prepare complex lists of objects, by
entering successive filtering conditions and pressing 
Ok
each time. The list 
Current thus obtained will be shorter
and shorter and will comply with all the conditions entered before.
When 
Scope is not 
Current, the selected objects that
are not yet members of the list 
Current are added to the beginning
of that list. Thus the list 
Current can be reduced by successive
filtering conditions of the 
Current list or increased by
successive additions from objects in other 
Scope lists.
Action
When 
Action is set to 
Include (the default), the next
Current list is formed by the atoms that have been selected
in the visible 
List on the left, using any available 
Method.
When 
Action is set to 
Exclude, the next 
Current
list is formed by the atoms that have not been selected in the visible
List.
Method
There are many different techniques to indicate which atoms should be
included or excluded to the list Current. The combo box 
Method
sets which technique should be used: 1) 
Pick, select one atom
each time, either pressing Ctrl and clicking on the atom visual representation
on a graphic area or pressing Ctrl and clicking directly on the atom tree
row on the 
List; 2) 
Region, select all atoms in a rectangle
in a graphic area (TODO); 3) one of the 17 remaining methods, representing
all the available atom properties.
In this case, for each property, a range of values should be entered in entries
Min and 
Max. When the value in 
Min is larger than the value
in 
Max, GAMGI swaps the two limits, issues a warning, and completes
the task. When 
Min is empty, only the 
Max condition is applied.
When 
Max is empty, only the 
Min condition is applied. When both
Min and 
Max are empty all values are accepted.
These properties can be combined to get the desired selection. For example,
to select a set of atoms between (x0, y0, z0) and (x1, y1, z1) just apply
the property 
X between x0 and X1, then 
Y between y0 and y1
and 
Z betweeb z0 and z1.
When no conditions are specified, by defaults all atoms are included
or excluded, according to the 
Action chosen. For example, to 
disable entirely a list of atoms previously selected, just open 
Atom->Select, change 
Action to 
Exclude and press 
Ok:
the color of the 
Atom label on the main menu changes to the
default color, signaling that no list of atoms exists.