OneAngstrom – Page 155

Permanent or Temporary? Making the Most of Measurement Labels in Molecular Modeling

Measuring distances, angles, and torsions between atoms is a common task in molecular modeling. It helps you validate structures, prepare simulations, and analyze chemical interactions. But if you’ve ever had to re-do the same measurement just because it disappeared when…

Filtering Molecular Models by Atom Counts: A Quick Guide for Structural Modelers

OneAngstrom

When working with large molecular datasets, one of the most common challenges modelers face is filtering out molecules based on their structural complexity. Whether you’re curating a dataset, setting up a simulation, or organizing your models, figuring out how to…

Understanding Selection Flags in SAMSON: What’s Actually Selected?

OneAngstrom

If you’ve ever found yourself puzzled by why a property model node appears selected (or not) inside SAMSON, you’re not alone. Understanding the difference between the selected attribute and the selectionFlag attribute can save time and confusion—especially when building automation…

Progressively Hiding Atoms for Clearer Molecular Presentations

OneAngstrom

In molecular modeling and presentations, visibility isn’t just about zooming or panning—it’s often about knowing what to show and when. A common obstacle faced by researchers and educators is how to direct focus within complex molecular structures. Showing too much…

Why You Can’t See That Atom: Understanding Visibility in Molecular Models

OneAngstrom

Have you ever loaded a molecular model, only to find that some atoms, bonds, or entire molecular groups seem to have vanished? If you’re working in SAMSON and this has puzzled you, you’re not alone. The cause is often related…

Choosing What You Click: Understand Selection Filters in SAMSON

OneAngstrom

When working on molecular systems with hundreds or thousands of atoms, fast and precise selection becomes critical. Do you really want to scroll endlessly or click around trying to highlight just the residues or atoms you care about? 🧬 In…

Running Python Scripts Directly in SAMSON

OneAngstrom

For molecular modelers who regularly write or experiment with small scripts to automate tasks or test algorithms, dealing with external script runners can be inconvenient. Switching between your molecular design environment and a text editor or terminal can break your…

From SMILES to 3D in Seconds: An Easier Way to Generate Molecular Structures

OneAngstrom

Turning a SMILES string into a reliable 3D molecular structure can often feel more complicated than it needs to be. If you frequently work with virtual screening, molecular docking, or QSAR modeling, you’ve likely spent too much time juggling between…

Quickly Find Chains by Atom Counts in SAMSON

OneAngstrom

When working with complex molecular models in SAMSON, it’s easy to get lost in the layers of structural information—atoms, residues, chains, segments, and so on. For molecular modelers, one of the most time-consuming tasks can be identifying specific chains based…

Avoiding Common Pitfalls When Creating Coarse-Grained Models with Multiple Protein Replicas

OneAngstrom

Simulating systems with multiple copies of a protein—such as membrane-bound proteins or protein condensates—is common in molecular modeling. Coarse-graining these systems using MARTINI force fields can significantly accelerate simulations, but there’s a critical step that often causes confusion: handling multiple…