Author: OneAngstrom

Molecular modelers often need to visualize complex structures where clear, distinguishable visual components enhance interpretation. Whether you’re color-coding residues, chains, subunits, or datasets, using carefully designed color palettes is key. Poor palette choices can make important elements indistinguishable, especially for…

Communicating molecular structures effectively isn’t just about showing atoms and bonds — it’s about delivering clarity. For molecular modelers, one persistent challenge is depth perception: distinguishing foreground and background parts in complex 3D structures. If you’ve ever struggled with interpreting…

When presenting molecular structures or simulating molecular processes, clarity is often key. Complex molecules with hundreds—or thousands—of atoms can easily overwhelm your audience and obscure the insights you want to share. Whether you’re preparing a lecture, building an educational video,…

When modeling molecular systems at the atomic level, selecting specific atoms based on quantitative criteria is often necessary—but rarely straightforward. Whether you need to isolate water molecules, highlight carbon atoms, or extract a structure within a geometric region, doing it…

Many molecular modelers often find themselves needing to align structures along specific axes or planes—whether it’s for preparing clean visuals, simplifying comparisons, or ensuring symmetrical arrangements for simulations. If you use SAMSON, you’ll be glad to know that aligning structures…

If you’ve worked with crystallographic protein structures, you’ve probably come across a common frustration: a PDB file only shows the asymmetric unit, not the complete biological assembly. This often leaves molecular modelers wondering how the actual protein complex is organized…

Protein-protein docking can be computationally intensive, especially when the search space is left unconstrained. If you know or suspect where a protein binding site lies, one practical way to speed up protein docking is by limiting the search domain. In…

When setting up a coarse-grained (CG) simulation with the MARTINI force field in GROMACS, many modelers run into a subtle but frustrating issue: unrealistic solvent packing that leads to simulation artifacts, often caused by solvent molecules overlapping with the solute…