OneAngstrom – Page 145

Smoothly Transition to Bound States with the Dock Animation in SAMSON

Creating meaningful molecular animations is often a pain point for modelers who want to illustrate molecular docking events or transitions between bound and unbound states. Animations can clarify biomolecular mechanisms in communication with collaborators, for publications, or for presentations. But…

Looking Down the Symmetry Axis: A Simple Way to View Molecular Interfaces

OneAngstrom

When working with large biomolecular assemblies like viral capsids or symmetrical protein complexes, finding the right perspective can make or break your design or simulation workflow. One overlooked but powerful technique is aligning your view along symmetry axes. The Symmetry…

Progressively Disappearing Atoms: A Clearer Way to Visualize Molecular Changes

OneAngstrom

When presenting complex molecular systems, clarity matters. Molecular modelers often face the challenge of showing transitions or drawing attention to specific molecular components without overwhelming the viewer with visual clutter. One common pain point is how to illustrate the step-by-step…

Making Molecular Animations More Manageable with NSL Attributes

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If you’ve ever worked on complex biomolecular systems in a dynamic context, you know that managing animations can be tedious. Whether you’re preparing a molecular movie or exploring simulation results, organizing and selecting the right animation elements matters. Fortunately, SAMSON’s…

When Hiding Helps: Using ‘Conceal Atoms’ for Cleaner Molecular Animations

OneAngstrom

Molecular modeling projects often involve creating visual presentations to highlight specific interactions, regions of interest, or structural changes. But when a model is too complex, clutter from surrounding atoms can obscure what really matters. If you’ve ever struggled to focus…

Quickly Generate Molecular Analogs with a Simple SMARTS Pattern

OneAngstrom

If you’re working in molecular design or drug discovery, you’ve probably come across the need to explore structural analogs of a lead compound – whether to improve binding, reduce toxicity, or evade metabolic vulnerability. Traditionally, this can require manual editing…

Filtering Residues by Charge in SAMSON: A Quick Guide for Molecular Modelers

OneAngstrom

When dealing with biomolecular systems, especially proteins, understanding the charge distribution of residues plays a critical role in many modeling tasks. Whether you’re preparing input for electrostatics calculations, identifying potential binding sites, or simply studying protein-ligand interactions, selecting residues based…

Avoiding Solvent Clashes in Coarse-Grained Simulations with GROMACS Wizard

OneAngstrom

When setting up molecular dynamics (MD) simulations using coarse-grained (CG) models, one recurring issue modelers face is improper solvation: water molecules overlapping with solute atoms or each other. This can happen easily when using default settings that are not tailored…

Making Molecular Components Appear on Cue in Your Animations

OneAngstrom

When creating molecular animations, one frequent challenge is controlling when specific components appear during your presentation. Whether you’re highlighting a ligand binding to a protein or the formation of a molecular assembly, the timing of element visibility is essential to…

Clicking Your Way Through Proteins: Inspecting Residues with the Interactive Ramachandran Plot

OneAngstrom

When working with proteins, even a single poorly-placed residue can make the difference between a stable simulation and a failed model. For molecular modelers, quickly identifying and fixing conformational outliers is more than just helpful – it’s essential. But in…