SAMSON Blog – Page 133

When Labels Block Clarity: Moving Them in SAMSON

When you’re working on complex molecular systems, clarity matters. Labels help provide context, highlight key elements, or annotate crucial measurements. But when too many labels crowd the Viewport or overlap with atoms and bonds, they can obscure what you’re trying…

Quickly Filter Molecules by Atom Types, Chains, or Residues in SAMSON

OneAngstrom

When working with complex molecular systems, modelers often face a common challenge: how to efficiently pick and analyze only the molecules that meet specific structural criteria. Whether you’re trying to extract smaller fragments from massive biomolecules or isolate candidates for…

Choosing the Right Colors in Molecular Modeling: A Look at Discrete Palettes in SAMSON

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One of the subtle pain points in molecular modeling is choosing effective colors that communicate your data clearly. Whether you’re differentiating chains in a protein, visualizing atom types, or building figures for publications, poor color choices can easily confuse viewers…

Label visibility in SAMSON: a quiet but powerful feature

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When working on complex molecular systems, visual clarity is key. Whether you are preparing figures for publication, designing custom visualizations for a client, or simply trying to study part of a simulation in better detail, controlling what is visible—and what…

Don’t Skip the Ions: Getting Coarse-Grained Systems Ready with GROMACS Wizard

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When running molecular dynamics simulations—especially in a coarse-grained (CG) setup using the MARTINI force field—preparation is key. One often overlooked but crucial step is ensuring your system is properly neutralized and has the right salt concentration. This blog post walks…

Orbiting Your Molecule: A Simple Way to Capture Better Molecular Visuals

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Molecular modelers often spend significant time preparing animations to showcase structural motions, interactions, or simply to produce high-quality visuals for sharing with collaborators or in presentations. But once the structure is prepared, how do you generate smooth, professional-looking camera movements…

Exporting Ligand Trajectories: Just the Atoms You Care About

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Molecular modelers frequently need to analyze how ligands move along defined pathways — whether for reaction coordinate studies, intermediate conformation extraction, or free energy calculations. But what if you’re only interested in the ligand, not the whole system? Exporting entire…

A Cleaner Way to Hide Molecular Structures in Animations

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Creating compelling molecular animations often requires precise control over the visibility of elements in your scene. Whether you’re showcasing a binding site, highlighting a conformational change, or simply guiding viewers through a molecular mechanism, what you choose to hide—and when—is…

Make Your Molecular Scenes Pop with a Simple Zoom

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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…

Keeping the Right Water: Efficient Cleanup of Crystal Waters in Molecular Simulations

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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…