Editing Atoms On the Fly While Simulating with UFF in SAMSON
Working with molecular models often involves tweaking structures to better fit expected configurations, eliminate artifacts, or explore structural variations. But what happens when you’re already mid-simulation, and you realize a modification is needed—say, removing a misplaced hydrogen, or adding a…
Saving Molecular Conformations and Trajectories with SAMSON’s Normal Modes Advanced
One common challenge in molecular modeling is capturing and comparing key conformational states during a simulation. Whether you are exploring structural flexibility, functional transitions, or designing ligands to fit various binding site shapes, keeping track of conformational changes is crucial.…
Quickly Find (or Hide) Molecules in Complex Scenes with NSL
Selecting Visual Presets in SAMSON: A Quick Guide with the NSL
When working on molecular models in SAMSON, visualization is often more than just aesthetics—it’s essential. Different render presets can highlight atomic structures, interaction networks, or molecular surfaces, which all help communicate scientific insight effectively. But when projects become complex, selecting…
Creating Smooth Transitions Between Protein Conformations with ARAP Interpolation
When studying protein dynamics, researchers often encounter an important question: how do we realistically interpolate between two known conformations of a protein structure? Whether you’re setting up umbrella sampling simulations or exploring conformational transitions for molecular docking, creating a smooth…
Quickly Explore Molecular Variants with Positional Analogue Scanning in SAMSON
When designing new drug candidates or optimizing a lead compound, molecular modelers often face the challenge of evaluating how small chemical modifications affect binding affinity, selectivity, or physicochemical properties. One effective approach to address this is positional analogue scanning, where…
