SAMSON Blog – Page 481

Making Molecules Fade In: A Clearer Way to Animate Visibility

Visual storytelling is powerful in science. Whether you’re preparing a presentation, recording a molecular event, or teaching a concept, the way components appear in your molecular model matters. If you’re working with molecular scenes in SAMSON, you might already know…

Choosing the Right Colors for Molecular Models: Discrete Palettes in SAMSON

OneAngstrom

When working with complex molecular models, color plays a bigger role than you might think. Color can help distinguish between molecular groups, highlight structural features, and enhance overall legibility—particularly in presentations, publications, or educational content. But picking colors manually can…

A Safer Way to Apply Custom MDP Parameters in SAMSON’s GROMACS Wizard

OneAngstrom

Applying custom simulation parameters in molecular dynamics (MD) workflows allows researchers to fine-tune their systems for specific scientific goals. But it can also lead to unexpected problems if those parameters are inconsistent or improperly set, especially when copied from other…

Why Only One Editor is Active at a Time in SAMSON

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For molecular modelers working with complex systems, a major challenge is managing various tools and functionalities without overwhelming the user interface. If you’ve ever wondered why SAMSON allows only one editor to be active at any given time, you’re not…

Getting Precise with Your Selections in SAMSON’s Document View

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For molecular modelers working with complex systems, selecting exactly the right groups of atoms, residues, or molecular fragments is often a repetitive and time-consuming task. Whether you’re preparing systems for simulation, analyzing interaction networks, or visualizing specific components, it can…

Quickly Find Hidden or Visible Models Using NSL in SAMSON

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If you are working with large molecular systems in SAMSON, you’ve probably faced the challenge of visual clutter. Hundreds of model nodes – some visible, some hidden, and many buried under layers of data. When you’re trying to focus on…

Selecting atoms with natural language in SAMSON AI

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Molecular modeling involves frequent selection of specific atoms, residues, chains, ligands, or binding sites. This task can become tedious and error-prone, especially in complex molecular systems. Traditional selection tools involve dropdowns, checkboxes, or writing selection syntax. Not only does this…

Quickly Identify Bonds by Type in Your Molecular Models

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When working with complex molecular structures, it’s often necessary to inspect or refine specific bond types, such as identifying only the aromatic bonds in a protein-ligand complex or checking for unusual bond patterns in generated conformers. This task, usually time-consuming…

Watching the SARS-CoV-2 Spike Move: A Useful Trajectory for Molecular Modelers

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Modeling conformational changes in large biomolecular assemblies is a recurring challenge in structural biology and drug design. One protein that drew intense focus is the SARS-CoV-2 spike, which transitions between closed and open states to interact with the ACE2 receptor.…

Why You Can Only Use One Editor at a Time in SAMSON

OneAngstrom

While working on molecular models, users often wish to interact with structures in more than one way—perhaps selecting atoms, applying transformations, and generating nanostructures all in succession. In SAMSON, this flexibility is achieved through Editors: tools designed to help you…