Accurately visualizing molecular and nanoscale systems can be a challenge, especially when trying to distinguish between different chains, residues or fields in a dense model. This is a common pain point for molecular modelers who need to both inspect and…

When working with molecular simulations, it’s common to want to track how specific parts of a system—like a ligand—move along a predefined path. This is especially important for tasks like reaction coordinate generation or free energy calculations. However, extracting only…

Selecting the right input files when moving from one molecular dynamics step to another can feel repetitive and error-prone. If you’ve spent time scrolling through directories, trying to remember the difference between several similar GRO files, you’re not alone. That’s…

Animations can play a crucial role in molecular design when you’re trying to communicate complex behaviors or structural transitions. But if you’ve ever found yourself trying to make parts of your molecular model appear at the right moment in an…

Creating compelling molecular movies isn’t just about showing structures. It’s about telling a story—moving the viewer through a sequence that makes complex molecular mechanisms clearer, behaviors easier to follow, and presentations more engaging. That’s where the Move camera animation in…

When generating interpolated paths between protein structures, it’s easy to forget one crucial step—structure preparation. If your structures contain water molecules, ligands, or disconnected fragments, the As-Rigid-As-Possible (ARAP) interpolation tool in SAMSON may fail with the error: “Cannot proceed because…

If you’ve ever struggled to interpret or share molecular models effectively due to unclear or inconsistent coloring, you’re not alone. Color plays a critical role in structure analysis—whether you’re trying to identify hydrophobic versus hydrophilic residues, distinguish chains, or highlight…