Running umbrella sampling simulations in molecular modeling can be complex, especially when dealing with dozens of starting conformations and ensuring consistency across multiple simulations. One challenge that many molecular modelers face is setting up those initial conformations and defining simulation…
If you’ve ever worked with protein simulation pipelines, you know that preparing a clean structure is foundational—but incredibly repetitive when dealing with large datasets. Whether it’s removing water molecules, adding hydrogens, or fixing alternate locations, these tasks consume time that…
When working with large molecular systems, biological macromolecules, or custom-designed coarse-grained models, quickly identifying specific structural components based on their chemical and structural properties can be a challenge. Whether you’re preparing simulations, visualizing data, or extracting substructures, manually selecting regions…
If you’re a molecular modeler, chances are you’ve spent a lot of time adjusting representations and color schemes just to get your visualizations to look right. From ribbons to atoms, VDW surfaces to chain coloring — great visuals often take…
When working with complex molecular systems, clarity is everything. Having the right labels—on atoms, residues, or entire molecules—can guide understanding and communication. But when you’re visualizing thousands of atoms, labels can quickly become overwhelming. Fortunately, SAMSON helps molecular modelers manage…
Sometimes, less is more—especially when creating animations to communicate complex molecular systems. If you’re working in SAMSON to design a molecular presentation or video, you might want certain molecules or nodes to vanish at key moments to maintain focus or…
As a molecular modeler, you might have experienced this situation: an update rolls out for your favorite modeling platform, and suddenly a plugin or workflow you depend on no longer works as expected. Or perhaps a collaborator is using a…
When working with complex molecular systems in SAMSON, it’s common to deal with hundreds or thousands of elements arranged hierarchically. Molecules include atoms, bonds, residues, and more. To model or visualize at large scale, molecular designers often hide or isolate…
When working on molecular modeling projects, searching for structural patterns within large biomolecules is often time-consuming. Whether you’re looking to identify highly charged side chains, filter out side chains with a large number of atoms, or isolate specific functional groups…
One of the less discussed, but surprisingly important aspects of molecular modeling is color perception. Visualizing molecular structures clearly is essential when working with complex systems, and when you’re layering atoms, molecules, or domains, using the right color palette can…
