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When working on complex molecular systems, visual clarity is vital. Whether you’re zooming in on a protein-ligand interaction or looking at the overall structure of a macromolecular complex, being able to shift perspectives quickly makes a difference. Fortunately, SAMSON offers…

Molecular modelers often face a common hurdle when setting up pulling simulations using GROMACS: how to define custom index groups that don’t appear in the default list. Whether it’s pulling a specific protein chain or restraining a certain region of…

One of the challenges in simulating real materials is going beyond the ideal crystal structure. In physical reality, materials often contain defects, which can completely alter their properties — from electronic behavior to mechanical resistance. Fortunately, the Crystal Creator extension…

Creating large or repetitive molecular structures manually can be a frustrating and time-consuming task, whether you’re building nanotubes, simulating repetition in crystals, or prototyping nanoscale machines. Many molecular modelers spend hours copying, rotating, and aligning fragments, often repeating the same…

When working with molecular dynamics simulations or exploring molecular mechanisms, it’s common to want to stay focused on a specific group of atoms as they move. Whether you’re tracking a ligand during binding, following a mobile domain during a conformational…

Any molecular modeler who’s ever tried to select a specific subset of atoms or residues in a large biomolecular structure knows the frustration: zooming in, clicking atom by atom, missing one, and starting over. But what if you could describe…

When presenting molecular animations, one common challenge is controlling when specific molecular components appear—and stay visible—throughout the timeline. This is especially important for molecular educators, researchers, and designers who create molecular presentations and want to seamlessly illustrate complex transformations without…

One of the biggest challenges in molecular modeling is producing visuals that are not only scientifically meaningful but also visually engaging enough for publications, grant proposals, or educational content. Whether you’re trying to highlight a catalytic site’s properties, showcase the…

When preparing biological systems for molecular dynamics simulations, one recurring dilemma is deciding which water molecules to keep—and which to remove. Some crystal waters are tightly bound or functionally important, especially in active sites. Others are just noise, cluttering your…