Section 2: Simplifying the view
As you have probably realised, it is difficult to see very much with this default (ball and stick) view of the structure. For this reason, Geneious provides a number of tools that manipulate the display.
Styles
Click on the
Style button and you will be offered a number of alternatives. Each applies to the selected atoms only but for the moment all atoms are selected. If not, click on the
Select box to the far right and click all.
- Hidden - hides all atoms
- Spacefill - display atoms as spheres the size of their van der Waals radii
- Ball and stick - default view showing bonds and atoms
- Wireframe - shows the bonds between atoms
- Sticks - similar to wireframe but with thicker bonds.
- Backbone - displays just the bonds of the α-carbon backbone
- Cartoon - follows the backbone but displays secondary structure elements
- Ribbons - similar to cartoon but as simple flat ribbons
- Rockets - replaces secondary structure with arrows
- Strands - like ribbons but not filled in
- Trace - follows the trace of the backbone without exactly matching the location of the atoms
- Dots - similar to spacefill but with dots rather than solid surfaces
- Mesh ribbon - similar to strands but more filled
Try these styles out for yourself.
Colors
Another useful feature is the ability to color structures.
- Default (CPK) - industry standard scheme representing atoms by specific colors. See http://en.wikipedia.org/wiki/CPK_coloring
- Fixed temperature - according to the temperature factor, a measure of the mobility or uncertainty of a given atom's position referred to an absolute scale of 0-100.
- Relative temperature - relative to the lowest and highest temperature factor values
- Amino Acid - colored according to traditional amino acid properties
- Chain - assigns each macromolecular chain a unique color.
- Formal Charge - colors atoms based on their formal charge, or ionic state
- Relative Charge - colors atoms based on their partial charge, or electron density
- Monomer - a reverse rainbow gradient used to color according to position along a chain starting with blue and finishing with red
- Shapely - colored according to the 'Shapely' coloring scheme
- Structure - Uses six different colors to distinguish four types of protein secondary structures and DNA vs. RNA.
- Plain Colors - simple colors that affect all selected atoms
Try combinations of styles and colors.
Select Backbone and Monomer. This is effective at showing the start and stop of the polypeptide chain. Combine this coloring with rocking the structure and you will have a good idea of how the linear primary sequence folds into the final tertiary structure.
Select Cartoon and Structure. Now you can clearly see the position of the secondary structure elements. You can see the α-helices and how the β-strands combine to form β-sheets.
Effects
Geneious provides some effects to improve the appearance of your structure or make it easier to see features.
- Spin - automatically rotates the structure in the window
- Antialiasing - smooth out rough edges making images more suitable for publication
- Slabbing - slice the front off a molecule so you can see the interior
- Stereo - cross-eye stereo giving a full color image in true 3D
- Stereo red/blue - uses traditional red/blue filter glasses to produce a 3D image
- Stereo red/green - Alternatively uses green filter for same effect
Section 3: Selecting parts of the structure
Section 4: Showing useful information