SAMSON Blog – Page 129

Quickly select molecular paths by number of atoms in SAMSON

When exploring or comparing molecular conformations, one common challenge modelers face is identifying specific types of paths—especially based on their complexity or size. For instance, locating paths that include a large number of atoms can help identify long chains, extended…

Stuck Exporting Molecular Data? Here’s What You Can Do in SAMSON

OneAngstrom

Whether you’re preparing a structure for simulation, sharing results with colleagues, or archiving your research, exporting molecular content is a routine — yet sometimes frustrating — part of computational modeling. Choosing the right format among PDB, XYZ, CIF, and others,…

Make Atoms Appear and Vanish in a Snap: Introducing the Flash Animation in SAMSON

OneAngstrom

When preparing molecular presentations or scientific animations, showing and hiding model components at the right moment can make all the difference. Whether you’re revealing specific binding sites, highlighting interactions, or walking through conformational changes, timing is essential. For many molecular…

Easily filter backbone groups by atomic composition in SAMSON

OneAngstrom

When building or analyzing molecular structures, modelers often need to focus on specific regions of molecules—like backbones with a certain number of atoms, or those containing specific elements. If you’ve ever found yourself manually clicking through complex molecular assemblies to…

From Pocket to Pathway: Defining Target Conformations in Protein Motion

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One of the recurring challenges in molecular modeling is understanding how a biomolecule—often a protein—transitions from one structure to another. Whether you’re studying loop movements that expose a binding pocket, domain shifts, or global conformational changes, capturing and controlling such…

Bring Molecular Models to Life with the Pulse Effect

OneAngstrom

Molecular modeling often involves communicating complex structural changes or emphasizing specific features of a model. But making molecules “pop” visually in presentations or animations can be tricky, especially when you want a dynamic and engaging representation that stays scientifically accurate.…

Identifying Charged Atoms in Complex Molecules: A Quick Guide with NSL

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When modeling molecules, identifying atoms with specific charges is vital in electrostatic interactions, pKa estimations, reactivity predictions, and more. Whether you’re building a molecular simulation from scratch or analyzing a protein-ligand complex, locating charged atoms quickly can save you hours…

How to Handle Bond Changes Interactively Without Breaking Your Model

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When building or modifying molecular structures, one of the most frequent roadblocks in molecular modeling is the difficulty of adapting molecular topologies on the fly. Typically, breaking bonds or introducing new connections means re-running perception algorithms or manually adjusting atom…

Fully Removing SAMSON from Your System: A Step-by-Step Guide for Every OS

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Whether you’re reinstalling, switching systems, or simply cleaning up your workspace, fully uninstalling specialized software like SAMSON can sometimes be more than a simple drag-and-drop. Many users in molecular modeling mention lingering files or confusion regarding leftover directories, settings, or…

Walking Backward Through Molecular Trajectories in SAMSON

OneAngstrom

Molecular modeling often involves exploring how molecules transition from one conformation to another. These trajectories can contain vital insights about the stability and behavior of biological systems, materials, or reactions. But what happens when you want to focus not only…