Integrated 3D molecule viewer

Viewing structure files

3D structures can be rotated, moved and zoomed with both the mouse and the keyboard.

At the bottom of the main 3D view area, a table can be shown with the included sequences and additional protein structures. This will reveal how many protein chains are present in a shown structure, and if other molecules are present. The sequence information may be copied from the 3D view with the purpose of further analyzing of the sequence by the other integrated tools in the Workbench.

3D Output

The output of the 3D viewer is shown on the screen in real time and changes to the layout are seen immediately. When the view has been adjusted to a preferred view, it is possible to export the graphics through the export menu.

Importing structure files

CLC’s workbenches support both pdb files and mmCIF files. These structure files may be imported in these ways:

• Download files from the Protein DataBank (http://www.rcsb.org) and import them as any other files.
• Search and download files through the integrated GenBank search function in the CLC Workbench.
• Select and download BLAST-hits resulting from BLAST-searches made towards the PDB database.

Options through the preference panel
The view of the structure can be changed in several ways. All graphically appealing changes are carried out through the View Preferences. The options in the View Preferences are

Atoms & Bonds

• Atoms (yes/no). Show the individual atoms as ball shaped structures. Different sizes can be set on the atoms.
• Stick (yes/no). Provide a stick between the atoms to visualize bonds.

Backbone

• Cartoon (yes/no). Show the backbone on proteins as cartoon drawings. When using this view it possible to see alpha-helices and beta-sheets.
• Backbone. Display the sequence of alphacarbons for all subunits.

Coloring

• Atom type (yes/no). Atoms are colored individually according to the Rasmol coloring scheme.
• Entities (yes/no). This will color subunits and additional structures individually. Colors for individual subunits may be set by the user.
• Rainbow (yes/no). This color mode will color the structure with rainbow colors along the sequence.
• Secondary structure. Residues that are part of beta-sheets or alpha-helices will be colored seperately.

Selection

• Highlight. Residues selected through sequence view will be highlighted with a brighter than usual colour.
• Inverse transparency. All other atoms than those that have been selected become transparent.

Other settings

• Quality. Image quality can be set to low, medium or high.
• Show water. This option allows water molecules to be seen in the view.
• Show table (yes/no). It is optional to show the table below the 3D view.