Author: OneAngstrom

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…

Presenting molecular structures to others can be a challenge, especially when static images fail to capture important spatial relationships and behavior. Whether you’re teaching, preparing a publication, or simply sharing a beautiful molecular system with your colleagues, clarity often lies…

Anyone working with biomolecular simulations knows the drill: you fetch a structure from the Protein Data Bank and it comes with water molecules — hundreds of them, sometimes thousands. The big question is: which ones should you keep? In many…