Author: OneAngstrom

When setting up a biomolecular system for simulation, one recurring challenge for molecular modelers is deciding what to do with water molecules already present in crystal structures. Should you remove them all, keep them all, or try to distinguish the…

Visual clarity is crucial when studying molecular structures. Whether you’re presenting a molecular mechanism or investigating the details of a ligand-binding site, your visual output must aid — not hinder — understanding. Fortunately, SAMSON offers an extensive set of rendering…

Have you ever run a protein-ligand docking simulation, only to find that the ligand doesn’t bind correctly—or worse, doesn’t bind at all? 🤯 Before diving into docking parameters or refining your scoring function, consider this: the problem might lie in…

Creating accurate molecular models is essential in nanoscience, especially when working with complex carbon-based structures like carbon nanotubes (CNTs). Yet, constructing customized multi-walled nanotube models can be surprisingly time-consuming in many modeling platforms. If you’ve ever wished for a more…

Building realistic lipid environments around membrane proteins can be challenging and time-consuming. Ensuring proper orientation of the molecule, avoiding atom overlaps, adding buffer space… these steps often involve a patchwork of tools and manual adjustments that take hours—even before you…

When working with complex molecular systems, it is often necessary to repeatedly check specific distances, angles or torsion angles between atoms. However, a common frustration among molecular modelers is the need to re-measure these values after every view change or…

If you’re a molecular modeler juggling multiple tools, supplementary data, scripts, or even presentation figures, you’ve likely experienced the frustration of losing track of crucial files. Whether you’re preparing a publication, sharing a molecular model with collaborators, or switching between…