Examples

The following examples give a sense of how bentopy can be used to build actual systems. We start with a very simple system, then demonstrate the powerful notion of combining compartments, before deriving a compartment from a vesicle structure by creating a space mask.

• Example 1: Simple sphere: In this example, we will first build a very simple system of lysozymes packed in a sphere.
• Example 2: Combining compartments: Then, we will add a compartment that allows us to fill part of the sphere with ubiquitin structures instead.
• Example 3: Masks from a structure: Finally, we will use a space mask derived from a vesicle structure, instead of an analytical sphere, demonstrating bentopy's ability to integrate different modeling strategies.

The goal of these examples is not to provide a completely hands-on tutorial. In fact, we have an excellent tutorial that shows the same concepts using models you can build yourself based on the provided starting files. Rather, these examples serve as a resource for people interested in learning about bentopy by example.