When preparing molecular animations or presentations, it’s common to need fine control over which parts of your model are visible at specific moments. Whether you’re explaining a ligand binding site, highlighting a subunit, or focusing attention step-by-step during a conformational…

Communicating how molecules come together can be a real challenge for molecular modelers. Whether you’re creating a teaching aid, preparing a presentation, or simply trying to highlight structural organization in a molecular system, the ability to animate the assembly process…

When preparing animations of molecular models, one of the most common challenges is producing smooth vertical camera motions that enhance understanding without distracting the viewer. For example, you may want to show a ligand slowly approaching a binding pocket, or…

Generating biologically realistic environments for membrane proteins is often a challenge in molecular modeling. One frequent task is preparing a lipid bilayer around a protein to simulate its behavior in a membrane-like system. Traditionally, this requires time-consuming scripting or the…

One common pain point in molecular modeling is accurately and efficiently defining the binding site for docking studies. Reproducibility, speed, and the likelihood of successful docking all rely on this small but critical step. Fortunately, for users of the FITTED…

One of the most common roadblocks in running production Molecular Dynamics (MD) simulations is selecting the correct input structure. A few missteps here can lead to errors mid-simulation or, worse, misleading results. Fortunately, the GROMACS Wizard in SAMSON offers a…

If you’ve ever worked on setting up molecular dynamics (MD) simulations with GROMACS, you’ve probably found yourself manually editing .mdp parameter files — sometimes copying from old projects, sometimes googling obscure keywords. For molecular modelers juggling complex systems, this process…

When preparing animations of molecular systems, one common challenge is smoothly revealing the components of a model to highlight transformations, interactions, or structural relationships. Molecular modelers often need to control how and when elements appear during visualizations to maintain clarity…

Many molecular modelers face the same issue when trying to present complex molecular structures or processes through animations: everything moves too quickly for their audience to follow 👀. You’ve likely spent hours crafting a presentation in SAMSON, carefully selecting keyframes…