Representations
Designed specifically for complex biological molecules, EasyHybrid offers a variety 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 GLarea selection menu (just click button 2 when a selection is active - see interface overview)
Let's explore the different ways EasyHybrid can represent atoms:
Wireframe Models: This basic representation displays atoms as simple lines connecting them, providing a skeletal framework of the molecule (default representation).
Sticks / Dynamic Bonds: As in lines, but represents connections in the form of sticks. In the "Stick" option, the bonds are immutable, in the "Dynamics Bonds" option, the bonds can break and form along a trajectory
Atomic Spheres: This representation depicts atoms as spheres centered at their atomic positions. The size is a fractional value of the 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 activated by selection, the representations are applied to all frames of the trajectory belonging to the selected object. They work in an additive logic, that is, the user can add new portions of a specific type of representation at different events, as well as remove them. The same logic works for color assignment. By default, carbon atoms are presented in the reference color of each system, however, the user can easily select specific portions of a model and assign different colors to the carbon atoms.
To change the color, simply select the desired group of atoms and access the "change" option in the GLarea selection menu (just click button 2 when a selection is active)
A window with the default GTK3 color palette will appear. This window may vary slightly from version to version. The selected color is assigned to carbon atoms only. The other atoms are represented by standard colors.
The user can add new portions of a specific type of representation at the same time as well change the carbon atoms' colors.
Different representation and different colors associated with different parts of the system of interest.