When working with complex molecular systems, you sometimes need to optimize just a portion of a molecule—such as a side chain, a loop, or a binding site—without disturbing the rest of the structure. Minimizing the entire molecule can lead to…

Mistakes happen 🧬. Whether you’re exploring a new protein conformation, editing a reaction intermediate, or simply rearranging atoms in your molecular design, it’s easy to misclick and lose a key step. Fortunately, SAMSON offers a dedicated History view feature that…

When working with complex molecular systems, modelers often need to isolate specific groups of atoms to perform targeted operations, run simulations, or build visualizations. One recurring task is selecting heavy atoms — that is, atoms that are not hydrogen. This…

When exploring molecular systems, molecular modelers often reach a turning point: they need to go beyond viewing and start editing atomistic properties. Whether for preparing simulations, constructing variants of a molecule, or cleaning up input data, changing a molecule’s internal…

When you’re designing molecular presentations, timing is everything. Whether you’re teaching, presenting to colleagues, or preparing a video abstract for a publication, manually toggling the visibility of molecular nodes can be time-consuming—and often results in jarring, unnatural transitions. This is…

When exploring molecular motions, one common challenge for modelers is how to effectively capture and reuse intermediate or final conformations. Whether you’re inspecting how a ligand access channel opens, or evaluating different configurations of a flexible loop, you often find…

When setting up a molecular system for simulation in GROMACS, atom group selections—known as index groups—play an important role in defining regions for restraints, analysis, and advanced sampling techniques like umbrella sampling. While GROMACS automatically generates standard index groups (e.g.,…

Crafting clear, visual molecular presentations often requires more than just beautiful molecules — context is important. If you’ve ever found yourself wishing your molecular animations could flow more smoothly between informational slides or contextual backgrounds, SAMSON’s Set background animation can…

When preparing molecular presentations, one frequent challenge is communicating spatial relationships without overwhelming the viewer with motion or detail. If a complex appears out of nowhere or its components aren’t clearly transitioning into place, the educational value can be diminished.…

One of the most time-consuming and repetitive tasks in molecular modeling is scripting. Whether you want to automate structure manipulation, calculate properties, or build custom GUIs, scripting remains essential—but not always straightforward. For many users, the hurdles range from not…