OneAngstrom – Page 305

Editing Molecules on the Fly: Dynamic Topology with IM-UFF

If you’ve ever tried to interactively modify molecular models during a simulation—adding atoms, breaking or forming bonds—you probably ran into the challenge of keeping energies consistent and topologies valid. For molecular modelers, working with fixed topologies can be limiting, especially…

Installing SAMSON Without Admin Rights: A Relief for Molecular Modelers

OneAngstrom

Installing scientific software can often be a frustrating process. Between admin privileges, system compatibility, and inevitable troubleshooting, molecular modelers often spend more time configuring tools than doing research. If you’ve encountered admin barriers—especially in institutional or academic settings where you…

Zero in on Conformations with a Specific Number of Atoms in SAMSON

OneAngstrom

When working with complex molecular systems, filtering large datasets to focus on specific structures can be time-consuming. For instance, identifying all conformations with a certain number of atoms might involve manual inspection or scripting — tedious or error-prone steps for…

Precise Atom Selection in Large Structures: An Overview of Symbol and Element Filters in NSL

OneAngstrom

When working with large biomolecular or material systems, selecting specific atoms is a routine but critical task. Whether you’re running simulations, defining substructures, or simply visualizing key components, manually identifying atoms by their type, symbol, or element quickly becomes inefficient.…

Easily Find Hidden Molecules in Your Model with Node Visibility Flags

OneAngstrom

When working with complex molecular models, it’s all too common to lose track of components that seem to disappear from view. Whether it’s atoms missing from a ligand or entire visual models vanishing without notice, navigating a crowded project in…

Running GROMACS Simulations in the Cloud with SAMSON

OneAngstrom

Setting up molecular dynamics (MD) simulations can be complex and time-consuming, especially when dealing with hardware limitations or compatibility issues. Running simulations on your own machine is not always feasible when dealing with large systems or long simulation times. If…

Bringing molecular scenes to life: camera animations in SAMSON

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If you’ve ever tried to present a complex molecular structure using static screenshots or default camera angles, you know how challenging it can be to convey 3D relationships clearly. Molecular modelers often spend hours setting up the perfect orientation, only…

Easily Filter Folders by Atom Counts in SAMSON

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If you’ve ever worked on a large molecular system in SAMSON, you know how challenging it can be to find the exact folders that contain specific subsets of data—especially when dealing with deeply nested models or extensive molecular datasets. One…

Display Atom Distances Instantly in SAMSON with This Shortcut

OneAngstrom

When building or analyzing molecular systems, one of the most common and necessary tasks is measuring distances between atoms. Whether you’re evaluating bond lengths, verifying docking poses, or checking geometrical constraints, distance measurements are essential to understand spatial relationships within…

Make Molecular Models Come Alive with the Rock Animation in SAMSON

OneAngstrom

When preparing molecular presentations, one of the most common challenges is getting viewers to intuitively grasp the spatial structure of molecular systems. Static images or models can fall short — especially when trying to convey subtle 3D features like binding…