Author: OneAngstrom

If you’ve ever faced the task of cleaning dozens—if not hundreds—of PDB files before running simulations or docking workflows, you’re not alone. Dealing with missing atoms, stripping waters, resolving alternate locations manually is not the most enjoyable part of molecular…

Working with large molecular systems often means wading through overwhelming layers of atoms, bonds, residues, chains, and structural groups. For molecular modelers and structural biologists, one of the most common tasks is to isolate particular regions of interest – ligands,…

When working on complex molecular models, selecting the right colors can make all the difference. Whether it’s to better highlight specific atom types, differentiate residues, or distinguish molecular groups, effective color use improves both clarity and communication. Yet, many molecular…

When working on molecular models, especially when exploring conformational changes, reaction pathways, or molecular dynamics simulations, it becomes essential to communicate these changes over time with clarity. This is where animations come in—not only as a presentation tool, but also…

Comparing entire protein structures can be useful – but sometimes, you only care about a specific segment. Whether you’re studying conserved motifs, flexible binding domains, or comparing specific helices across two species, aligning full structures may dilute the insights you’re…

When working with large molecular systems, sometimes your goal isn’t to minimize the entire structure. Instead, you may want to refine only a selected part of a molecule, like a side chain in a protein, a ligand in a binding…

When working in molecular design, collaboration and visibility can open many doors: partnerships, contributions, opportunities, recognition. Yet, many molecular modelers overlook a simple step that connects them to the global research community: creating their public profile on SAMSON Connect. If…

Molecular modelers spend considerable time optimizing molecular geometries – making sure atoms are in the right place, bonds have the correct length, and everything aligns with physical reality. But clicking through optimization steps and waiting for calculated results can feel…

Creating custom carbon nanotube structures can be a time-consuming and repetitive task, especially when modeling them atom-by-atom. Fortunately, with the integrated pattern editors in SAMSON, you can build nanotubes from scratch in just a few steps — while staying in…

One common challenge in molecular modeling is creating meaningful transition pathways between two conformations of a protein. Whether you’re studying allosteric mechanisms, conformational flexibility, or receptor–ligand induced fit, identifying and selecting the correct starting and target shapes can be one…