SAMSON Blog – Page 180

When Downloaded Structures Aren’t Ready: Dealing with Missing Atoms and Residues

Working with publicly available protein structures can feel like opening a surprise package. Sometimes, it’s all there — chain complete, atoms in place, ready for simulation. More often, though, it’s not. Missing heavy atoms, absent side chains, incomplete backbones, protonation…

Let Your Molecular Animations Breathe: How to Pause with Purpose Using the Stop Animation in SAMSON

OneAngstrom

When crafting molecular animations, timing is everything. Whether you’re presenting a mechanism of action, illustrating a conformational change, or giving a live seminar, controlling the pace of your animation helps your audience absorb complex processes one step at a time.…

Getting more signal from your notes: Use the ‘selected’ attribute efficiently in NSL

OneAngstrom

When juggling multiple structures, annotations, and visual states in a molecular project, keeping track of what’s selected and what’s not can quickly become a point of friction. For modelers who use notes to mark hypotheses, highlight anomalies, or trace ideas…

Running GROMACS Simulations on 100 Conformations? Here’s How to Do It in One Go

OneAngstrom

If you’ve ever needed to simulate the same molecular system under multiple conformations — for example, in Umbrella Sampling or conformational ensemble simulations — then you probably know how time-consuming it can be to prepare each conformation manually. Good news:…

How to Keep Atoms Still While Everything Else Moves

OneAngstrom

In molecular modeling and animation, we often focus on what moves. However, sometimes what doesn’t move is just as important. For molecular modelers who want to control which parts of a molecule are in motion and which remain static, SAMSON…

Need a Previous Version of SAMSON? Here’s How to Install It

OneAngstrom

If you’re working on a scientific project that relies on a specific version of SAMSON for compatibility reasons — perhaps due to an extension that was developed for an older API, or to reproduce simulation results — reinstalling a past…

Making Molecular Models More Readable with Visibility Flags

OneAngstrom

In molecular modeling projects, clarity matters. Whether you’re preparing a figure for publication 🧬 or inspecting large biomolecular structures, clutter can make it hard to analyze or present your data. One common issue modelers face is toggling visibility efficiently across…

Quickly Show or Hide Labels in SAMSON Using NSL

OneAngstrom

In complex molecular scenes, quickly identifying and toggling label visibility can dramatically enhance your workflow in SAMSON. Whether you’re preparing a presentation, reviewing a molecular model, or debugging a simulation, being able to control which labels are shown (or hidden)…

Smooth Transitions in Molecular Animations: How to Tweak Path Playback in SAMSON

OneAngstrom

Visualizing molecular motion can be challenging—especially when reviewing complex structures or conformational changes. Many molecular modelers spend unnecessary time interpreting trajectory data frame by frame, struggling with jerky transitions and inconsistent playback speeds. If you’ve found yourself in this situation,…

Never Render Blindly Again: Understanding Light Node Visibility in SAMSON

OneAngstrom

When you’re managing complex molecular systems in SAMSON, ensuring that your scene renders exactly what you expect is critical—especially when working with lighting. However, debugging visibility and selection issues for light sources can be frustrating, especially in scenes with multiple…