OneAngstrom – Page 367

Finding the Right Molecular Modeling Tools in the SAMSON Extension Marketplace

One of the most common challenges for molecular modelers is finding the right tool for a specific task—especially when working with a complex system that requires specialized functionality. Whether it’s parsing a new file format, creating a unique visual model,…

Quickly Toggle Light Node Visibility in Your Molecular Scene

OneAngstrom

Working with complex molecular scenes often means toggling various types of nodes on and off to simplify visualization, focus on relevant components, or prepare publication-ready images. While atoms and molecules get most of the attention, lighting nodes play a crucial…

Opening Molecular Pockets Using Normal Modes: A Practical Workflow

OneAngstrom

Controlling the conformation of a biomolecule to open or close a binding site is often a challenging step in molecular modeling. Whether you’re setting up a drug docking simulation or analyzing conformational flexibility, being able to guide molecular motion toward…

Making Molecular Models Fade Away: Using the Disappear Animation in SAMSON

OneAngstrom

When showcasing complex molecular systems, clarity is key. Elements in the foreground may obscure parts of the structure you want to highlight, and simply hiding them can feel too abrupt. That’s where the Disappear animation in SAMSON becomes valuable: it…

Progressively Hiding Atoms to Highlight Molecular Mechanisms

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In molecular modeling and education, revealing just the right amount of detail at the right moment is crucial. Whether you’re preparing a presentation or building an instructional animation, visual clarity can make or break how well a concept is understood.…

Creating Custom Index Groups in GROMACS Wizard Without Breaking Your Workflow

OneAngstrom

When working with molecular simulations in GROMACS, you often rely on index groups to define subsets of atoms. GROMACS generates standard ones automatically—like protein, water, or ions—but what if you need more control? Whether you’re setting up biased simulations or…

A Practical Guide to Setting Up Custom Index Groups for Pulling Simulations in GROMACS Wizard

OneAngstrom

Setting up center-of-mass pulling simulations in GROMACS often requires the definition of custom index groups—particularly when dealing with multi-chain protein systems. For many molecular modelers, this step introduces friction, especially if you’re switching between the command line and visualization tools.…

Position, Click, Animate: A Practical Guide to Keyframe Motion in Molecular Models

OneAngstrom

In molecular modeling, dynamic presentations can help clarify complex mechanisms far better than static images. Whether you’re illustrating a potential drug interaction, conformational change, or even just repositioning molecules to highlight geometry, animations go a long way in explaining scientific…

Quickly Filter Molecular Node Groups with NSL Selection Attributes

OneAngstrom

Depending on the size and complexity of your molecular system, selecting and filtering parts of the model can easily become one of the most repetitive and time-consuming tasks during molecular modeling. If you’ve ever found yourself endlessly clicking between interface…

Tired of Losing Atom Paths? Here’s How to Capture Them Reliably in Your Molecular Animations

OneAngstrom

One of the recurring challenges in molecular presentations is preserving how atoms move during a simulation or an animation. Whether you’re docking molecules, assembling structures, or applying custom motion, understanding and showcasing atomic trajectories is crucial. But what happens when…