within a self-assembled aggregate if it spans one or more dimensions of the simulation box and if the aggregate is larger than a half of the length of the simulation box in one or more dimensions. Figure (a) shows a polymer micelle that has spanned the simulation box in at least two dimensions. Failing to accurately reproduce structures across the PBC can lead to inconsistencies in the analysis and interpretation of soft matter systems. In contrast, the PySoftK make_micelle_whole tool is able to accurately represent the coordinates of molecular structures which span the PBC, even if their size is greater than half the box size. More details about this algorithm are described in the ESI. Therefore, make_micelle_whole provides an accurate representation of the system, which ensures that any physical properties of the self-assembled structure and its environment is calculated correctly. For example, certain functions of MDAnalysis, such as radius_of_gyration() or moment_of_inertia(), may produce erroneous results when applied to molecules and aggregates that span at least a single dimension, leading to artefacts in the simulation analysis. For instance, Figure shows the difference between using solely the MDanalysis radius_of_gyration(pbc=True) function (Figure Auxiliary Functions. We have included a number of smaller functions to perform simple analysis tasks in a unified way. These are briefly described below.