Author: OneAngstrom

When working on molecular systems, it's common to need to inspect or adjust properties of atoms, residues, or other entities—often not just one by one, but in groups. Whether you’re refining a simulation input, validating a structure, or preparing a…

When working in molecular modeling, quickly grasping the identity or role of individual elements—atoms, chains, ligands, or other entities—is essential. Yet, it’s surprisingly easy to get lost in a sea of similar shades when visualizing complex systems, especially when you’re…

When working with complex molecular systems, visual communication becomes key—especially when creating presentations or recording animations for colleagues or publications. A common need for molecular modelers is to pan the view horizontally without altering the orientation or zoom level of…

One of the most frequent pain points in protein-protein docking is the overwhelming number of false positives that can result from broad, unconstrained docking searches. If you already have some structural knowledge about your proteins—like the approximate location of binding…

Removing water molecules before running a molecular dynamics simulation can be more complicated than it sounds. For molecular modelers working with crystal structures, deleting all waters indiscriminately can result in the loss of functionally important waters, especially those located in…

One of the unexpected challenges researchers face in academic or enterprise environments is software installation restrictions. If you’re working on shared, secured systems, you may not have administrator rights. This can create frustrating bottlenecks when installing tools essential to your…

Selecting specific atoms in a large molecular model can feel like finding a needle in a haystack. Whether you’re filtering by element types, location, or charge, traditional tools can be tedious and error-prone, especially when selections need to be repeated…

When it comes to molecular dynamics simulations, one size rarely fits all. Whether you’re optimizing a protocol, reproducing a published study, or trying to match specific experimental conditions, modifying your simulation parameters is often essential. But editing .mdp files by…

Understanding molecular interactions often requires not just static snapshots of a system, but watching how molecules move—especially when investigating mechanisms like ligand unbinding or conformational transitions. One common challenge for computational chemists and molecular modelers is the need to export…