Author: OneAngstrom

Managing atom groups in molecular dynamics is crucial when preparing a simulation, especially when fine-tuning analysis protocols or defining dynamic groups like pull coordinates. One sticking point for many modelers is knowing when and how to add custom index groups…

When visualizing molecular designs, motion tells a powerful story—highlighting transitions, conformational shifts, or dynamic interactions with clarity that static images can’t match. But creating smooth, accurate animations can often seem like a hurdle, especially when working with molecular systems where…

When working with complex molecular structures, navigating a 3D environment efficiently can save time and effort. It’s common for molecular modelers to find themselves constantly adjusting the view—zooming into a reaction site, switching to a side angle, or stepping back…

As molecular modelers, we often work with many moving parts: molecular structures, scripts, analysis data, figures, and draft papers. Keeping all of these project components synchronized across machines—or sharing with collaborators—can become an organizational challenge. Fortunately, SAMSON‘s Universal File Embedding…

Tracking how ligands move through molecular systems — such as during unbinding or along diffusion pathways — is often a challenging task for molecular modelers. The movement can be complex, and visualizing it clearly across multiple frames of a trajectory…

Managing data in molecular modeling workflows can become overwhelming. Scripts, models, images, experimental results—these often reside in scattered folders across different machines. This increases the risk of broken references, version confusion, and forgotten dependencies. If you’re using SAMSON, the integrative…

It’s a common frustration for molecular modelers using the SAMSON platform: you install an extension like the Nanotube Creator, eager to build carbon nanotubes for your simulation, only to be puzzled when nothing new appears in the interface. Where is…

One of the most common tasks in molecular modeling is selecting specific atoms or residues within complex biomolecular systems. Whether you’re preparing a simulation, visualizing sidechains, or analyzing interactions, precision in selection is essential. Yet, many molecular modelers waste valuable…

Color is more than aesthetics in molecular modeling – it’s a key part of communication. Whether you’re distinguishing chains in a biomolecular complex or visualizing multiple residues, choosing the right discrete color palette can make your visualizations clearer and easier…

One of the recurring challenges in molecular modeling is how to visually explore and present complex nanosystems. Whether you’re designing a macromolecular assembly, analyzing electron density data, or preparing figures for a presentation, you’ve probably wished for better control over…