Author: OneAngstrom

When working with protein modeling pipelines, one task that can quickly become repetitive and error-prone is formatting and cleaning your input structures. Whether you’re setting up simulations, docking experiments, or dataset-wide screening tasks, the protein structures you start with need…

Predicting the structure of protein-ligand complexes from NMR data often requires significant manual effort, especially when dealing with unassigned methyl peaks. The combinatorial nature of the problem can quickly become overwhelming: Which methyl belongs where? How do distance restraints from…

When presenting complex molecular models, timing is everything. Whether you’re guiding students through a conformational change or highlighting a catalytic site in a biomolecule, viewers need time to absorb key visuals. This is where the Pause animation in SAMSON becomes…

Visualizing molecular systems over time is a key aspect of effective scientific communication, especially when building presentations or educational material. One frequent need among molecular modelers is to illustrate the gradual disappearance of parts of a system—say, to focus attention…

Building accurate models of carbon nanotubes (CNTs) for simulations or experimental planning can be time-consuming, especially when dealing with multi-walled configurations. For molecular modelers exploring structural, mechanical, or transport properties of CNT-based systems, being able to quickly generate these models…

When exploring and presenting molecular structures, visual clarity can make a significant difference. Molecular modelers and science communicators often need to rotate a molecule to showcase its shape, symmetry, or orientation relative to other molecules or fields. But executing this…

When fine-tuning molecular structures, one common challenge is minimizing only a subset of atoms without disturbing the rest of the system. This might be needed, for example, when adjusting a flexible loop in a protein or fixing a local geometry,…