OneAngstrom – Page 338

Reduce Eye Strain When Modeling Molecules: A Look at SAMSON’s Dark Mode

Staring at bright screens for hours can be exhausting — especially for molecular modelers who often spend long sessions analyzing complex structures. Whether you’re building interaction models, rendering simulations, or working late into the night, eye fatigue is a common…

Make Molecules Fade Away: When ‘Disappear’ Is Better Than Hide

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When creating molecular animations for presentations or publications, molecular modelers often face the challenge of showing molecular structures gradually vanish—without making it look abrupt or confusing for the audience. While the classic ‘Hide’ effect can switch off visibility instantly, sometimes…

Filtering Molecular Chains by Attributes in SAMSON’s NSL

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When analyzing complex molecular structures, it’s often necessary to selectively work with specific parts of a system — for example, focusing on protein chains with a certain number of residues or minimizing visual clutter by displaying only visible chains. This…

Controlling Visibility in Molecular Models: A Hidden Time-Saver

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When working with complex molecular systems, clarity is essential. Modelers often juggle large graphs with nested structures, annotations, and auxiliary nodes like notes. In SAMSON, the integrative platform for molecular design, note nodes can be used to organize, label, and…

Quickly Align Protein Structures Based on Specific Residue Regions

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When exploring protein function or designing ligands, it’s often essential to compare specific functional regions, rather than entire protein structures. This is especially true in structure-based drug discovery, homology modeling, and evolutionary studies, where conserved motifs might be hidden among…

Precise Bond Filtering in Molecular Models Using Bond Types

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When working on large molecular systems, it’s often helpful to focus only on specific types of bonds—such as single, double, or aromatic bonds—especially when analyzing or modifying chemical structures. Whether you’re identifying functional groups or cleaning up imported models, being…

Selecting Cameras with Precision in SAMSON’s Node Specification Language

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In complex molecular modeling projects, scenes often contain a variety of cameras—top views, side views, custom perspectives for presentations, or analytical views for simulations. Managing these cameras efficiently can become challenging as projects grow in size. The Node Specification Language…

A Simple Way to Align Molecular Structures in SAMSON

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When working on multi-component molecular systems—such as protein-ligand complexes, nanostructures, or assembling ligand libraries—being able to precisely align and position structures is essential. But manual alignment can be both time-consuming and error-prone, especially when scaling operations or ensuring consistency across…

How to Spot and Fix Strained Protein Residues with an Interactive Ramachandran Plot

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One of the recurring challenges in protein modeling is ensuring that your structure is biologically plausible before advancing to simulations. Even after refinement steps, it’s not uncommon to stumble upon strained residues — local backbone conformations that fall outside allowed…

Smart Importing of Molecular Dynamics Results: A Quick Guide

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Running molecular dynamics (MD) simulations is only half the work—the other half is interpreting and importing your results correctly. Many molecular modelers face the recurring challenge of efficiently handling large MD simulation data, especially with regards to choosing what to…