Visualizations

Basics

Catana enables to visualize both fully atomistic and coarse-grained structures using various representations. The representations span various abstraction levels, enabling to choose the most suitable one for the given scenario. Moreover, the representations can be dynamically modified by

• changing the selected color scheme and color scale,
• rendering only desired parts of the structure,
• or coloring selected parts with a desired color.

Single component can be visualized using multiple representations at the same time, allowing for highly customizable visuals.

Filtering

The selection-based features rely on a filtering language, enabling to write textual queries specifying the parts to be affected.
Accessing the Filtering help window in the Help option of the navigation bar provides list of commands potentially usable for the filtering. The outcomes of filtering depend on the type of structure (all-atom versus coarse-grained), as well as on the selected visual representation (for example, some representations like cartoon cannot show just a single residue).

Filtering examples

Following filter string will show only guanines from chain A.

:A and DG

In comparison, following filter string will show all chains except chain A.

not :A

Finally, this filter string shows only residues 460 to 465 of chain B and all alanine residues.

(460-465 and :B) or ALA

Figure below shows a structure visualized using two different representations. The user modified the cartoon representation to highlight residues 13 to 29 in blue and residues 144 to 155 in red. Then, the user filtered out the ball-and-stick representation to show only alanine residues. Moreover, all alanine residues were further highlighted in green, except the Ala65 highlighted in yellow to emphasize its location.

Sequence visualization

To give the users possibility to examine primary sequences of visualized structures, Catana provides Sequence view available in the Inspector submenu. This editor allows to visualize sequence of the arbitrary chain of the desired structure. Moreover, as shown on the image below, the sequence can be colored according to the current colors of the 3D scene to provide 1:1 correspondence between 3D visualization and the sequence.