OneAngstrom – Page 133

Quickly Find Atoms by Element, Oxygenation, or Geometry in SAMSON

In molecular modeling, it’s common to need specific subsets of atoms for tasks like analysis, visualization, or simulation. For example, you might want to display only the oxygen atoms in a protein, exclude hydrogens, or select planar aromatic carbons. Performing…

From Red to Green: Making Sense of NMR Restraints in Molecular Models

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One common challenge when working with NMR-derived molecular structures is ensuring that NOE distance restraints are actually satisfied in the resulting models. While tools for applying restraints exist, it’s often hard to see what’s going on—especially when dealing with multiple…

Running Python Scripts in SAMSON: What You Need to Know

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Many molecular modelers rely on scripting to streamline repetitive tasks and develop custom workflows. One common challenge, however, is finding a molecular modeling platform that allows direct execution of scripts — particularly Python scripts — without switching between environments. If…

Instant Molecular Beauty: A Guide to Visual Presets in SAMSON

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Communicating complex molecular systems often requires more than just structural accuracy—it demands clarity and readability. As a molecular modeler, you might spend valuable time adjusting colors, representations, and visual styles to produce a publication-ready image. What if you could do…

How to Define Reactive Sites for Analogue Generation Using SMARTS Patterns

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When designing new molecular analogues, chemists often wonder: Which part of the molecule should I modify to explore new activity profiles? In early-stage drug design, this is one of the most frequent roadblocks. If you’re interested in systematic molecular modification,…

Quickly Identify Complex Paths in Large Molecular Models Using NSL

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When working with large molecular systems, it’s often necessary to filter out simpler conformations and focus on more complex molecular substructures. For example, in DNA-protein complexes, signaling pathways, or molecular machines, paths containing a high number of atoms can represent…

Controlling Label Visibility in Molecular Models with NSL

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When working with complex molecular models, clarity is key. Whether you’re preparing figures for publication, sharing a model with collaborators, or simply trying to declutter your workspace, the ability to selectively show or hide label nodes can make a significant…

Stabilizing Your View in Molecular Simulations: The ‘Look at Atoms’ Feature in SAMSON

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When working with complex molecular trajectories, a common challenge is keeping your focus on a specific region of interest. Atoms may move, conformations may shift, and before you know it, your camera has lost track of the very part of…

Make Your Molecules Breathe: Highlighting Dynamics with the Pulse Animation in SAMSON

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A common challenge in molecular modeling is effectively communicating complex 3D structures and dynamic behaviors to both colleagues and broader audiences. Whether for presentations, publications, or teaching, clarity and visual engagement are key – and this is where animations shine.…

A Clearer Way to Design Polymer Sequences: Fewer Errors, Better Control

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If you build custom polymers for molecular modeling, you’ve probably dealt with challenges when specifying complex monomer sequences. How do you know your defined sequence is valid? Have you correctly designated bond types between monomers? Are your naming conventions traceable?…