Tutorials:Display Types

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This tutorial will deal with some display types of molecules including : Wireframe, Ball and Stick, Cartoon, Ribbon, etc.

Configuration: Avogadro version: 1.0.0

For this purpose we have chosen the human insulin model to play with. But this work can be done with any other protein.

Getting started

First, download this 1hiu.pdb file.
Open the saved 1hiu.pdb file with the menu File > Open or press Ctrl+O.
The molecule will appear in the View 1 panel with a default display type (previously chosen), for example, the Ball and Stick mode as shown below:

Ball and Stick display type - Grey: carbon, red: oxygen, blue: nitrogen, yellow: sulfur

To navigate switch to Navigate Tool by choosing it from the toolbar or by pressing F9. Using the mouse or the keyboard, you can zoom, rotate and slide the molecule. To recenter the molecule in the field, choose View > Center or (shortcut ?).
Optionally, hydrogen atoms can be removed using Build > remove hydrogens.
In the display types menu (the left panel) you can see the available display types listed with checkboxes:

Ball and Stick selected in display types panel

Atoms with the minimum radius

Atoms with the maximum radius

By clicking on the Settings (the small wrench icon beside the display type) you can customize the appearance. For instance, the Ball and Stick settings gives you many choices such as:
- atoms radius
- bonds radius
- opacity, very useful if you want to superimpose many display types
- display or not display of valence (double bonds)

Ball and Stick settings

Now we will visualize the protein residues or amino acids.
- select the Stick display type and deselect Ball and Stick or any other
- Open Stick settings
- In Colors tab, choose colorize according to residue in the upper drop-down list and amino acids color pattern in the lower one. The result should be as below:

Stick display type with highlighted amino acids

In order to recognize residues names, we can easily display the labels. To do so, select Label in the display types menu and in its settings select residue name from atoms label drop-down list.

Labels display.

Now, let's try to visualize only one residue and identify its positions in this polypeptide chain. For this purpose, we will make selection of a specific amino acid for example let's take the Leucine abbreviated as LEU. In Selection menu choose Select by Residue..., write LEU in the output box and click OK. Then, in the Objects tab from the Stick settings choose display only selected primitives. As a result, we should obtain the display of 6 Leucine residues:

Displaying only Leucine residues