Author: OneAngstrom

When analyzing molecular simulations or designing dynamic molecular experiences, it's often helpful to explore how systems behave in reverse. Whether you want to retrace a folding pathway, investigate a transition state return, or simply generate a looping presentation between conformations,…

For many molecular modelers working on editing or designing molecular systems, a common challenge lies in how to dynamically change the structure of a molecule while maintaining computational stability and physical consistency. Actions as simple as dragging an atom to…

When creating animations of molecular systems, there’s often a subtle challenge that becomes painfully clear during presentations: showing the right part of the system at the right moment. Molecular modelers regularly struggle with visual clutter that hides key mechanisms or…

For many molecular modelers working in academic or corporate environments, the ability to install software without administrator rights isn’t just a convenience—it’s a necessity. Whether you’re using a restricted machine or working remotely where IT support is limited, not having…

If you’ve ever tried to animate a molecular system, you’ve probably faced this: you want to show certain parts of the molecule moving, while others remain still. But without a way to fix parts of the structure, animations can quickly…

Obtaining a reliable set of initial conformations is a common challenge when setting up umbrella sampling for free energy profile calculations. Whether you’re working with protein-ligand systems or studying molecular interactions along a reaction coordinate, getting this step right is…

When preparing molecular simulations, getting the right topology can be a time-consuming task. While automatic perception of bond orders and atom types is helpful, most modelers eventually hit a point where they’d like more control: maybe the automatic perception misses…

Constructing nanotubes manually can be a tedious and error-prone process for molecular modelers. Aligning rings, duplicating atoms, merging structures, and optimizing geometry often requires significant time and care—especially if relying on custom scripts. In this post, we’ll show an alternative…

One of the most common pain points for molecular modelers is the constant need to juggle multiple tools, plugins, and scripts across different platforms just to get one workflow done. What if all of those tools could be brought directly…

When working on complex molecular systems, it’s common to switch between multiple regions of interest. You might be analyzing a ligand binding pocket, adjusting side chains of a receptor, or inspecting solvent placement. Repeatedly reselecting these components adds friction to…