SAMSON Blog – Page 49

Why You Might Want to Stop and Breathe During Your Molecular Presentation

Molecular modelers often spend hours perfecting animations that communicate complex mechanisms and structures with clarity. When showing a ligand docking process or a protein folding simulation, even a few fast-moving frames can disrupt the viewer’s ability to keep up. This…

Freezing Atoms to Minimize Only What Matters

OneAngstrom

Interactive molecular minimization in SAMSON is convenient and fast, but what if you’re only interested in minimizing part of a molecule—say, just a few atoms or a flexible side chain—without altering the rest of the structure? When setting up a…

Recording Atomic Movement in Molecular Animations: Efficiently Capture Atom Paths in SAMSON

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When working on molecular presentations, especially those that involve atomic movements such as docking, assembly, or simulation, demonstrating atom trajectories can significantly improve clarity and understanding. But how do you precisely capture those trajectories for presentations and further analysis? This…

Finding the Right Chains Fast in Your Molecular Model with NSL

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When working with large molecular systems, it’s easy to feel overwhelmed trying to isolate the chains that matter most for your research. Whether you’re targeting specific biomolecular chains for visualization, simulation, or export, filtering them manually can quickly get tedious…

Avoiding the Pitfalls of Importing NPT Equilibration Results

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In molecular dynamics simulations, a well-managed NPT equilibration is only half the journey: importing the results correctly can be just as critical. Many researchers using GROMACS encounter confusion or inconsistencies at this stage—not because their simulation failed, but because pressure…

Visualizing Ligand Unbinding Paths with Energy Profiles in SAMSON

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Molecular modelers studying protein-ligand interactions often get stuck after generating ligand unbinding paths: how do you analyze these trajectories, compare them, and extract valuable information such as energy barriers? If you’ve used the Ligand Path Finder in SAMSON, the good…

Quickly Find the Right Structures Using Folder Attributes in SAMSON

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When working with large molecular systems, it’s common to collect data into folders: protein complexes, membrane aggregates, ligand groups, solvent structures, etc. But when your SAMSON document has dozens—or even hundreds—of folders, how do you efficiently find the ones you…

Controlling Focus in Molecular Visualizations with Depth of Field

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Molecular modelers often struggle with visual clutter when working with large biomolecular systems. Zooming in on an area of interest can still leave the background fully detailed and distracting, which makes presentations or publications less effective. A simple yet powerful…

How to Share Molecular Workflows as Executable Files in SAMSON

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Sharing a molecular model with collaborators often comes with a familiar headache: supplementary scripts are in a separate folder, dependent files are missing, and paths break across systems. As molecular modelers, we frequently juggle multiple files—models, data, Python scripts, results—and…

Is Your Molecular Model Too Flat? Try Ambient Occlusion in SAMSON

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When you’re working on a molecular model, getting the science right is step one. But communicating it effectively—especially visually—is just as important. A common challenge molecular modelers face is that 3D structures often appear flat and hard to interpret due…