[ENHANCEMENT] Save modified trajectory visualisation settings

**Is your feature request related to a problem? Please describe.**
At the moment it is possible to change the radii of atoms or the colours of atoms and background. However, the changes are not permanent and can be undone by switching to another trajectory.

**Describe the solution you'd like**
We can use the configuration file of the Trajectory tab to store the changes.

**Describe alternatives you've considered**
Should this be done for all trajectories, or per trajectory? Should the changes be saved **in** the trajectory file?

**Additional context**
The main question is if the users want to change the appearance of all their trajectories at the same time, or to make each one of them different.

Start by reading how the Trajectory tab configuration stores visualisation settings and how switching trajectories currently resets them. The issue names no files or tests; determine first whether settings should apply to all trajectories or be stored per trajectory, then define persistence behavior for atom radii and atom/background colours.

Written by the indexing model from the issue text.