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When preparing molecular presentations or animations, clarity and focus are everything. Whether you’re showcasing a binding site for clarity, highlighting a ligand interaction, or trying to subtly direct the viewer’s attention, camera movements go a long way. But have you…

When preparing biomolecular systems for molecular dynamics simulations with GROMACS, one common but confusing step is deciding what to do with crystal water molecules. Should all crystallographic water be deleted? What if some are essential to the protein’s function? This…

Staring at brightly lit interfaces late at night while working on detailed molecular structures can be tiring and distracting. For molecular modelers who spend hours analyzing complex geometries, renderings, and atomistic simulations, eye strain caused by bright themes is a…

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…