Author: OneAngstrom

One of the frequent challenges faced by molecular modelers using umbrella sampling is the often cumbersome post-processing stage required to compute the Potential of Mean Force (PMF). The actual simulation might already have been computationally expensive, but without a streamlined…

Creating compelling molecular animations can help researchers explain mechanisms, analyze behavior, and communicate results more effectively. But if you’ve ever tried to animate groups of atoms rotating around their center with precision, you’ve probably dealt with scripting or manual workflows…

Selecting atoms one by one is often the first bottleneck in setting up a molecular experiment or simulation. Whether you’re defining a region of interest, modifying a subset of atoms, or preparing geometric restraints, manual selection can become slow and…

If you’re working in molecular modeling, you’ve likely found yourself repeatedly diving through hierarchies of chains, residues, and atoms to apply selections—especially when dealing with large biomolecular complexes. These selections may be necessary to analyze binding sites, investigate side chain…

If you’ve ever tried to import a structure file into one tool, only to export it for another, you know the pain: data loss, conversion issues, and a lot of time spent trying to figure out which formats are supported.…

When working with complex biomolecular systems, navigating 3D structures to select specific residues can be time-consuming and error-prone. Whether you’re preparing a simulation, designing a mutation, or analyzing a structural motif, efficient residue selection matters. Fortunately, SAMSON offers a synchronized…

When manipulating molecular structures, it’s easy to make small changes that have big consequences—like accidentally moving an atom… or several. If you’ve ever found yourself wondering how to precisely adjust or revert attributes of different parts of your molecular model,…

When sharing molecular models—whether it’s for a presentation, a publication, or simply collaboration—clarity and consistency matter a lot. Screenshots taken from visualization software are often inconsistent in size, format, or even visibility due to cluttered interfaces or unsuitable backgrounds. If…

For many molecular modelers, selecting specific parts of large molecular structures—residues in a chain, atoms in a binding site, or side chains near a ligand—can be a recurring bottleneck. Traditional selection involves manually clicking through models or crafting complex queries…