SAMSON Blog – Page 161

How to Smoothly Play Molecular Trajectories in SAMSON

Visualizing molecular dynamics or conformational changes often requires playing through a defined trajectory or a series of saved conformations. But if you’ve ever tried to animate a path manually or synchronize multiple structural transitions, you probably know how frustrating and…

Turning Simulations into Slide Decks: Using the Stop Animation in SAMSON

OneAngstrom

Molecular modelers often spend countless hours creating compelling simulations and animations that showcase molecular dynamics, binding events, or structural rearrangements. But when it comes time to present these simulations in a structured, slide-like format—especially for lectures or reports—it becomes tricky…

Making Molecular Models Appear or Disappear: A Look into Visual Visibility Attributes

OneAngstrom

When working on complex molecular systems, visual clarity is essential. Whether you’re preparing a figure for publication or curating snapshots for a presentation, chances are you’ve had to hide or reveal parts of your molecular model. But which parts should…

Too Many Simulations Running? Here’s How to Monitor Your GROMACS Jobs in SAMSON

OneAngstrom

Running molecular dynamics simulations can often feel like juggling. You launch one equilibration job… then another… and before you know it, you’re wondering what has finished, what is still running, and where the results were saved. If you’re using the…

Revealing the Hidden Depths: A Look at Progressive Clipping in SAMSON

OneAngstrom

Exploring complex molecular structures, such as large proteins or densely packed nanomaterials, often presents a recurring challenge for modelers: internal features get visually buried inside layers of atoms. Rotating and zooming might help, but more often than not, you lose…

Missed a Bad Angle? Use This Visual Trick to Spot Strained Residues Instantly

OneAngstrom

If you’ve ever run a molecular dynamics simulation only to encounter unexpected behavior, there’s a good chance you’re not alone. While energy minimization and restraints can catch many issues, a far more visual—and proactive—tool can help with one common modeling…

Quickly Filter Visible Lights in Molecular Scenes with NSL

OneAngstrom

When working on complex molecular models, managing visualization elements such as lights can become overwhelming. Whether you’re lighting your scenes for rendering or just tidying up your workspace, it’s crucial to be able to filter and isolate visible elements efficiently.…

Filtering Bonds by Type in Molecular Models: Practical Tips for Better Selections

OneAngstrom

One common challenge faced by molecular modelers is isolating meaningful subsets of bonds in complex structures. Whether you’re designing a molecule, analyzing structural motifs, or customizing visualizations, you often need to select specific bond types without manually clicking through thousands…

Installing SAMSON Without Admin Rights: What You Need to Know

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Installing powerful software for molecular modeling often comes with a common challenge: administrator rights. For many students, researchers, or professionals working on institutional computers, the inability to install software without admin privileges can be a blocker. But if you’re looking…

Selecting Ligand, Active, and Fixed Atoms for Unbinding Pathway Exploration in SAMSON

OneAngstrom

When exploring ligand unbinding pathways from proteins, molecular modelers often find themselves struggling with a deceptively simple question: which atoms should I select as the ligand, the active motion drivers, or the fixed anchors? The outcome of your unbinding simulations…