Knowledge of the three-dimensional (3D) atomic structure of materials is essential to a fundamental understanding of their properties. The key to understanding the functionality of many materials, particularly those of commercial and industrial interest, is often hidden in the details at the nanoscale. For this reason, it is very important to choose the right strategy to analyze the structure of challenging materials with complex disordered framework structures, or of the layered materials that are the subject of this thesis. Structure analysis of beam-sensitive or uniquely disordered materials can be complicated. Although there are already existing methods such as X-ray powder diffraction (XRPD), the data may exhibit reflection overlap or ...