Author: OneAngstrom

One of the most common frustrations when visualizing molecular systems is the repetitive and time-consuming process of manually applying visual styles and color schemes. Whether you’re preparing figures for a presentation, teaching structural biology, or analyzing large biomolecular complexes, you’ve…

When working with large molecular systems, one of the most time-consuming tasks for molecular modelers is selecting specific atoms or groups of atoms based on precise geometric or chemical criteria. Manual selections can quickly become unmanageable, especially in dense structures…

When refining a protein model—whether from homology modeling, docking, or simulation—chances are you’ll encounter a few residues out of place. These are often exposed on a Ramachandran plot as positions falling into disallowed regions, indicating strained backbone conformations. How can…

As a molecular modeler, your workflow often depends on integrating the right tools at the right time. SAMSON helps streamline activity through its modular approach using SAMSON Extensions. Learning how to add, try, subscribe to, or remove these extensions can…

One of the challenges in protein modeling is evaluating and refining backbone conformations efficiently. While molecular simulations offer deep insights, visual and interactive tools can bring clarity and speed to pre-simulation structure validation. Imagine identifying problematic residues and correcting them…

Setting up molecular dynamics (MD) simulations can be time-consuming and error-prone, particularly when it comes to managing parameters and ensuring simulation consistency. If you’ve ever struggled with mismatched thermodynamic coupling parameters or forgotten to adjust the number of steps before…

When communicating complex molecular structures, clarity is everything. Whether you are generating animations for a publication, presentation, or teaching materials, you often need to emphasize specific regions of a molecular system. But what if you want to get closer to…

Creating compelling molecular presentations can be time-consuming—especially when you want to visually demonstrate how molecules interact. A common challenge for structural biologists and molecular modelers is to simulate docking mechanisms with clarity and realism, for publications, teaching, or presentations. Fortunately,…

Molecular modelers often need to compare different structural states of a molecule—whether it’s to analyze intermediate steps of a simulation, visualize reaction pathways, or share reproducible milestones in a modeling workflow. However, managing these snapshots within a single project has…

One of the common challenges in molecular simulations is running the same GROMACS workflow (minimization, equilibration, simulation) across multiple conformations of the same molecular system. Whether you’re performing an Umbrella Sampling study or simply exploring the conformational landscape, repeating the…