Tutorials:Making selections
From Avogadro
Contents |
Introduction
Making selections is an important operation when using Avogadro.
- Deleting the selection
- Using Display Types for parts of the molecule
- Adding hydrogens to only the selected atoms
- Moving the selected items in space
- ...
There are several ways to make selections. However, the easiest or quickest way often depends on the task you are trying to accomplish. While the selection methods in this tutorial are organised in 3 sections, you can (and are encouraged) to mix these methods while working with Avogadro.
Before continuing this tutorial, make sure all necessary plugins are enabled. If you just installed Avogadro these will be enabled by default. Otherwise you can use the video below to help you enabling the Selection Tool and Selections Extension. Setting up the project three will be explained later.
Selections Extension
The "Selections" Extension provides many selection methods accessible through the Select menu. Since the first two items are frequently needed, short-cuts are provided.
Select All Ctrl+A Select None Ctrl+Shift+A
At any point, you can delete the currently selected items by pressing the Backspace key.
Invert Selection
Inverting the current selection is often useful when making selecting which will be assigned to display types (see next tutorial). For example, if you have selected all ligands in a protein complex and assigned it to a display type (e.g. Stick). Inverting the selection will select the protein which can then be assigned to a different display type (e.g. Simple Wireframe)
Select SMARTS
[SMARTS] are usually used for subgraph searching. The select SMARTS function in Avogadro selects all matched atoms in the molecule. All [SMILES] are valid [SMARTS]:
SMILES Description C(=O)O select all carboxylic acids, esters, ... N select all aliphatic nitrogen atoms n select all aromatic nitrogen atoms n1ccccc1 select all atoms in pyridine rings
[SMARTS] are much more powerful though. Here are some examples using SMARTS that cannot be expressed as a single SMILES:
SMARTS Description a1aaaa1 select all aromatic atoms in 6 membered rings A select all aliphatic atoms [O,N][#6] select all ON and NC fragments (O & N are aliphatic, C can be aliphatic or aromatic)
More information on how to write SMILES and SMARTS strings can be found here:
[SMILES - A Simplified Chemical Language] [SMARTS - A Language for Describing Molecular Patterns]
Select by Element
Clicking the "Select by Element..." action will show a periodic table. Clicking any of the elements in the table will select all atoms for which the atomic number matches the clicked element.
Select by Residue
This option allows you to select all residues with a specified residue name (e.g. "VAL", "TYR", ...). While the VAL and TYR example might not be of great value, this option can often be useful for selecting ligands with a known name. For example, the 1DRF.pdb protein contains a folate molecule with residue name FOL.
1DRF.pdb:
... HET FOL A 187 32 ... HETNAM FOL FOLIC ACID ... FORMUL 4 FOL C19 H19 N7 O6 ... ATOM 1508 N1 FOL A 187 26.779 12.325 -3.996 1.00 0.00 N ATOM 1509 C2 FOL A 187 27.684 12.453 -5.033 1.00 0.00 C ATOM 1510 NA2 FOL A 187 27.113 12.270 -6.218 1.00 0.00 N ...
Uisng the select by residue option, it is easy to select the ligand. Once selected, a display type can be assigned to the ligand. When using the cartoon display type for proteins, selections are rendered as wireframe in the selection color (Figure 3).
Select Solvent
Currently, only residues with the name HOH are selected.
Selection Tool
While all previous select methods didn't involve the 3D widget directly, clicking on atoms and bonds to make selections is possible using the Selection Tool. The selection tool has 3 modes:
- Atom/Bond: Select the clicked atom/bond
- Residue: Select the residue to which to clicked atom/bond belongs. This only works for molecules with residues like proteins for example. Both the atoms and the bonds of the
residue will be selected.
- Molecule: Select all atoms and bonds connected to the clicked atom/bond.
The Atom/Bond mode is exclusive without using modifier keys. This means when you click various atoms consecutively, only the last will be selected. This behaviour can be changed by holding the Shift (or Ctrl) modifier key while clicking the atom/bond.
- Shift (Add modifier): Select additional atom/bond without deselecting any previous selection. When clicking on an already selected atom, this has no effect.
- Ctrl (Toggle modifier): Same as Shift but deselects a selected atom/bond when clicking on it.
Both Residue and Molecule mode work in a toggle like way. Clicking a previously unselected residue/molecule will select it, clicking it again will deselect it. (note: these modes don't use modifier keys)
There is one more option for making selections using this tool. Left clicking on an empty space in the 3D widget and moving the mouse cursor will draw a selection box. When the mouse button is released, all atoms and bonds inside the box will be selected. The modifier keys can also be used with selection boxes:
- Shift (Add modifier): Select additional atom/bond without deselecting any previous selection.
- Ctrl (Exclusive modifier): Select only the atoms and bonds within the box. Previous selections will be deselected.
Named Selections
Once a selection has been made, it can often be useful to make it a named selection using Select > Add Named Selection.... This allows for quick reselection later using the Project Tree.
Selecting and the Project Tree
If the project tree is not visible, it can always be made visible again using Settings > Toolbars > Project Tree. If the project tree is empty, items can be added using Settings > Configure Avogadro... (Figure 5). This only needs to be done once, the settings will be stored for later sessions. Some of the items you can add are User Selections, Molecule, Atoms. In the real project tree, these items will expand and contain the actual selections, residues, items and so on. Double clicking an item will select the matching atoms, bonds, ... (Figure 6).
