Author: OneAngstrom

Preparing realistic molecular environments around membrane proteins can be a time-consuming task. Building lipid bilayers manually, aligning structures, avoiding bad contacts — this setup work often becomes the bottleneck before simulation even begins. If you’re using SAMSON, there’s a dedicated…

Designing and manipulating molecular models often requires different types of interactions: creating new structures, selecting parts of a system, or applying transformations. A common hurdle for molecular modelers is smoothly switching between these editing actions without having to dig through…

When modeling molecules, selecting specific atoms, residues, or groups based on their relationships or properties can make or break your workflow. Whether you’re preparing a system for simulation or analyzing structural features, having to sift through thousands of atoms manually…

When creating coarse-grained models from protein structures using the MARTINI force field, researchers often need to simulate multiple replicas of the same protein. For example, building a molecular box of repeated protein units is a common setup in membrane protein…

One common challenge molecular modelers encounter is knowing exactly when a system is truly ready for simulation after running equilibration steps. After all, launching a full-blown molecular dynamics (MD) simulation on an unstable system can mean wasted hours—or even days—of…

When creating molecular animations to explain a mechanism or guide an audience through a complex structural change, timing is everything. One common challenge for molecular modelers and scientific communicators is how to effectively reveal parts of a molecule to focus…

When presenting molecular mechanisms or simulating transitions in a complex system, clarity and pacing can often make or break the message you aim to deliver. Molecular modelers frequently struggle to communicate intricate step-by-step behaviors within molecules—especially when animations move too…

When working with complex molecular systems, it’s common to want to optimize the geometry of only a specific part of a molecule—without disturbing the rest of the structure. This can be especially useful during refinement workflows, local repairs in crystal…

When visualizing complex molecular systems, even small movements in camera angles or target positions can create confusion. You may want to zoom in on a receptor-binding pocket, for instance, without altering the perspective or the background. Maintaining a fixed target…

One common challenge in molecular modeling is visualizing conformational changes between known states of a complex biomolecule—especially when those changes reveal key biological functions, such as viral infection mechanisms. If you’ve ever worked with large protein structures that undergo dramatic…