Author: OneAngstrom

A common challenge in molecular modeling is not just generating motions, but storing them in a meaningful and shareable way. Whether you’re communicating your results to colleagues, preparing figures for publication, or organizing data for further analysis, saving conformational changes…

When working with covalent inhibitors, many molecular modelers face uncertainty: preparing bond order, dealing with hybridization, and ensuring correct interaction setup can be complex and error-prone. If you’ve ever needed to dock covalent ligands (like irreversible inhibitors) but were unsure…

One of the recurring challenges for molecular modelers is illustrating and analyzing the conformational changes of large biomolecular structures. When representing motion between two conformations—like open and closed forms of a protein—preparing a realistic and useful trajectory can be time-consuming.…

When preparing molecular presentations, one common challenge is how to *introduce* a complex structure in an intuitive, scientifically accurate, and visually pleasing way. Whether you’re building a talk, creating a research video, or teaching protein assembly, it’s hard to beat…

Carbon nanotubes (CNTs) are remarkable structures used in nanotechnology, materials science, and even drug delivery. But building them manually in a molecular editor can be tedious and error-prone—especially when dealing with atomic-level precision and numerous repetitions. In this post, we’ll…

When running molecular simulations using the Universal Force Field (UFF), one common challenge modelers encounter is the automated typization of atoms. While automatic typization is practical, it doesn’t always fit specific system constraints or user expectations. SAMSON offers a solution…

Creating clear and informative molecular animations can be surprisingly time-consuming. For molecular modelers and presenters, one recurring challenge is how to control the visibility of molecular components across time without making the transitions distracting or unnatural. Whether you’re preparing an…

When you’re building a molecular animation in SAMSON — maybe you’re docking a ligand, assembling a structure, or simulating a dynamic system — it’s common to run into this problem: you want to show where your atoms have been, but…

Starting a DNA origami project from scratch is often time-consuming, especially when you’re iterating on existing concepts. That’s why the ability to import pre-existing designs can be a game-changer for molecular modelers. If you’ve used Cadnano in the past and…