5.7.4 Proteins

In addition to the standard display styles, the two protein specific displays of C-Alpha Traces and Ribbons are supported. Examples of these display styles can be seen in Figure 5.6.

**Figure 5.6:** Different views of the same protein
[Wireframe] [C-Alpha Trace] [Ribbon]

Given that protein files often inevitably contain many extra components that are not necessarily of interest to the user (waters for example), the ability to hide the display of non-bonded atoms is provided to ease the viewing of proteins without having to manually edit the input file. An example of a protein displayed with and without waters can be seen in Figure 5.7.

**Figure 5.7:** Same protein with and without waters
[Protein with Waters] [Protein without Waters]

These protein specific display styles are controlled in the Proteins section of the Molecules page of the Style Window (see Figure 5.3). This section contains three rows of three buttons each.

In the first row, the buttons turn on the display of c-alpha traces, protein ribbons, and residue labels respectively. Residue labels are text labels attached to the alpha carbon of each residue which contain information about the type of residue associated with the labelled atom. In the second row, the buttons turn off the display of c-alpha traces, protein ribbons, and residue labels respectively.

In the third row, the first two buttons launch dialogs which allow customization of some of the important parameters in the generation of c-alpha traces and protein ribbons respectively. The third button toggles the display of non-bonded atoms in the scene as mentioned above (see Figure 5.7).

**Figure 5.8:** Same protein as a single molecule vs as multiple molecules
[Multimer displayed as a single molecule] [Multimer displayed as multiple molecules]

Another common scenario when working with proteins is that the input file contains a large multimer which as expected is interpreted as a single molecule. However, sometimes the ability to interact with the individual components is of particular value. The ability to split a molecule into separate components can be performed by selecting the ``Components" option in the ``Split Molecule" submenu in the Edit menu. This function will then determine what the individual components of the Focused molecule are and create a new list containing a new molecule for each component. The original molecule is not changed or deleted. An example of this process can be seen in Figure 5.8. The ``Split Molecule" submenu also contains ``Selected" and ``Marked" options which will create new molecules from the original based on the selected or marked set of atoms.

				VIDA User Manual

				VIDA User Manual