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Designed specifically for complex biological molecules, EasyHybrid provides a wide range of tools to visualize these intricate structures.
To change the type of representation, simply select the desired group of atoms and access the "Show" option in the GL area selection menu (just click Mouse Button 2 when a selection is active — see interface overview).
Let’s explore the various ways EasyHybrid can represent atoms:
Wireframe Models: This basic representation displays atoms as simple lines connecting them, providing a skeletal framework of the molecule. It is the default representation.
Sticks / Dynamic Bonds: Similar to the line representation, but shows connections as sticks. In the "Stick" option, bonds are fixed, while in the "Dynamic Bonds" option, bonds can break and form along a trajectory.
Atomic Spheres: This representation depicts atoms as spheres centered at their atomic positions. The size of each sphere corresponds to a fraction of the atom’s van der Waals radius.
Ribbons or Cα Trace: This representation is particularly useful for visualizing protein structures. It displays the protein backbone as a continuous ribbon or trace.
Wireframe for Non-Bonded Atoms: This representation depicts atoms that are not directly connected by covalent bonds using a wireframe model (for mono atomic species).
van der Waals Spheres: This representation depicts the entire van der Waals radius of each atom, providing a more complete picture of the molecule's overall size and shape.
When a selection is used to activate a representation, it is applied consistently across all frames of the trajectory for the selected object. Representations follow an additive logic—users can incrementally apply different representation styles to various parts of the system over time, and remove them as needed. This same additive approach also applies to color assignment.
By default, carbon atoms are colored using the system’s reference color. However, users can easily override this by selecting specific regions of a model and assigning custom colors to the carbon atoms.
To change the color, simply select the desired group of atoms and choose the "Change" option from the GL area selection menu (just click Mouse Button 2 when a selection is active).
A window with the default GTK3 color palette will appear. This window may vary slightly depending on the version. The selected color is applied to carbon atoms only; all other atoms are displayed using their standard colors.
The user can add new portions with a specific type of representation and simultaneously change the color of the carbon atoms.
Different representations and colors can be associated with different parts of the system of interest.
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