Another instance is the portrayal of potential orientations of ligands within a binding pocket of a protein and their spatial proximity to crucial active site residues. A third example is that a researcher might want to demonstrate how specific functional groups within a molecule exhibit closer spatial proximity under particular environmental conditions than would be inferred solely from their skeletal structural formula. In all these instances, graphical representations hold the potential to convey information far more effectively and intuitively than an extensive textual description. Fortunately, a multitude of software applications are readily available to aid scientists and researchers in crafting three-dimensional visualizations of molecules. Among the noteworthy tools in this domain are Jmol , 3Dmol.js , Blender [3], and PyMOL , each offering distinct capabilities and features for the visualization and analysis of molecular structures.