There are many ways to select atoms in GaussView.
We will demonstrate several here, including: Mouse-based selection
The Atom Selection Editor Expanding Selections
Selecting by PDB Residue and Using the Atom List Editor for Selecting
We begin with selecting atoms using the mouse.
There are 3 mouse selection modes: click mode, rubberband mode and brush mode.
Click selection is useful for selecting individual atoms within a complex molecular structure.
Here we select 3 methyl groups in Taxol by clicking on them individually.
You can enter click selection mode using the corresponding toolbar icon.
You can also use click selection at any time by holding down the C key when clicking.
Rubber band selection allows you to drag a rectangle—also known as a marquee—around
the desired areas of the molecule.
Here, we drag selection rectangles over the atoms in two rings.
You can use rubberband selection at any time by holding down the R key.
The brush selection tool is useful for quickly selecting atoms in a dense structure.
To use the brush tool, we click and drag over the atoms we want to select.
You can use brush selection at any time by holding down the B key.
There are two more selection-related icons and keystrokes.
To select all atoms, press the A key, or use the Select All icon.
To deselect all atoms press the N key, or use the Select None icon.
In addition to the mouse-based selection modes, we can also create and modify selections
with the Atom Selection Editor, which is opened with the Tools ---> Atom Selection menu path.
The Atoms Selection Editor allows us to: set the current selection mode,
to change the default behavior of the selection tools,
to expand the selection outward, and to perform other complex operations using
selections.
This section of the dialog contains options for the mouse-based selection modes.
They enable and disable various selection behaviors.
For example, the Additive Rubberband Selection option is on by default.
Each use of the rubberband adds to the current selection.
When we deselect Additive Rubberband Selection, each use of the rubberband replaces the current
selection.
For example, when we select the benzene ring, the previously-selected methyl group is deselected.
As the controls in the editor indicate, all three modes have optional deselection abilities.
However, this behavior is only enabled for Click mode by default.
We enable it for rubberband mode as well by selecting the corresponding checkbox.
We’ve also re-enabled Additive selection for rubberband mode.
To demonstrate this feature, we first select all of the atoms in the Taxol molecule.
Then when we drag the rubberband around a portion of the molecule, the atoms within
the marquee are deselected.
In general, the selection state of each atom within the marquee is toggled when rubber
band deselection is enabled: selected atoms are deselected and unselected atoms are added
to the current selection.
With the Expand Selection tool, we can enlarge a selection to include the atoms adjacent
to the already-selected ones.
Adjacent atoms can be identified by bonds, by absolute distance or by PDB Residue.
For example, when we expand the selection by Bond, each movement of the slider expands
the selection outward to all atoms that are bonded to each currently selected atom.
When we expand by Distance instead, each expansion adds the atoms within a certain distance of
each selected atom regardless of bonding.
The behavior of the slider is controlled by the up to field to its right.
This sets the sliders maximum value, that is the number of bonds or the distance in
Angstroms that corresponds to moving the slider all the way to the right.
For example, when it has the value of 10 bonds, moving the slider all the way to the right
selects all atoms within 10 bonds of any initially-selected atom.
At any point, the Atoms field at the bottom of the dialogie displays the atom numbers
of all selected atoms.
For molecular structures imported from PDB files, selection can also be performed by
PDB residue.
We’ve already opened the Atom Selection Editor.
We continue by selecting the Tools->PDB Residue menu option.
In the PBD Residue Editor, we scroll to residue 66, which is part of the active site for this
molecule.
We select this row.
Next, we select Generally-Select Atoms of Selected Rows from the Rows menu which says
to select all of the atoms for the residues in each selected row of the table.
In our case, this selects the atoms in residue 66.
In order to expand the group of atoms, we will use the Atom Selection Editor.
The Using popup is set to PDB Residue, starting from the initially selected residue, each
use of the slider adds the next adjacent residues in the sequenced to the selection.
Here, we change the display options for the selected atoms to allow you to see them easily.
In our final example, we demonstrate using the Atom List Editor to easily select atoms
of a certain type.
In this case, we want to select all of the hydrogen atoms within this uranium compound
except those in the methyl group bonded to the central uranium atom.
We open the Atom List Editor using the corresponding item on the Tools menu.
The atom list is a table of all atoms in the molecule, their structural parameters and
other attributes.
Since we want to select hydrogen atoms, we will sort the list by element.
We click on the Symbol column to select it.
We then open the Rows menu and choose its Sort Selected->Ascending by Symbol option.
Now the table is sorted by element.
In this case, all of the hydrogen atoms in the molecule appear first.
We want to ignore hydrogens 4, 5 and 6, as those are the methyl group hydrogen atoms.
We select the table rows for atoms 34 through 87.
Then we click Generally-Select Atoms of Selected Rows on the Rows menu, and the desired hydrogen
atoms are selected.