OneAngstrom – Page 58

Export Atomic Coordinates Along a Ligand Pathway: A Simple Way to Prepare Reaction Coordinate Files

Tracking the motion of molecules in a system can be crucial for understanding mechanisms like ligand binding and unbinding, conformational changes, or for generating reaction coordinate files in free energy methods. If you’ve been manually extracting coordinates along a path,…

Filtering Conformations by Atom Count in Molecular Models

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If you’ve ever worked with large molecular systems, you know how quickly the number of conformations in a project can become overwhelming. Whether you’re analyzing protein dynamics, running conformational ensembles, or simply loading a PDB with alternate locations, data clutter…

What Makes an Animation Visible?

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Working with complex molecular animations in SAMSON can get tangled fast. One common frustration that molecular modelers face is when an animation node doesn’t appear in the viewport — even though it seems like it’s supposed to. You might have…

Synchronizing Molecular Trajectories with the Play Path Animation

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Watching molecular systems in motion can be incredibly helpful for understanding complex conformational changes, analyzing reaction mechanisms, or conveying structure-function relationships. But making professional animations from molecular paths can sometimes feel like a chore—especially when working with multiple trajectories that…

Quickly Find Structures with Specific Atom Counts in SAMSON

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Molecular modeling often involves managing large datasets with complex structural hierarchies. If you’re working in SAMSON and using folders to organize molecules, residues, or atoms, you may have run into the challenge of locating specific entities based on detailed characteristics…

Why Your Molecular Animation Might Be Too Fast (and How to Fix It)

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Have you ever prepared a beautiful molecular animation, only to realize that important steps fly by too quickly for viewers to follow? Animations help molecular modelers communicate complex transitions—such as ligand binding, protein folding, or molecular docking—but without proper timing,…

Seeing Molecules: A Straightforward Guide to Visual Models in SAMSON

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For molecular modelers, visual clarity can make or break a project. Whether you’re inspecting protein structures, analyzing electrostatic surfaces, or preparing materials for publication, you often need to translate invisible concepts into intuitive images. That’s where visual models become essential…

Oops in Molecular Modeling? How to Backtrack Safely in SAMSON

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When working with molecular models, experimentation is essential — but mistakes are inevitable. Whether it’s an accidental deletion, a misalignment, or even just curiosity to explore alternate paths, having the ability to retrace your steps without losing progress is crucial.…

From 2D analogs to 3D molecules in seconds: A quick route to structural insight

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Creating analog libraries is a common part of early-stage molecular design or virtual screening workflows. But what happens once you have a list of 2D chemical analogs—how do you go from a SMILES representation to three-dimensional molecular models ready for…

Why Understanding Symmetry Can Accelerate Your Protein Simulations

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Running simulations on large protein assemblies can be computationally expensive. But what if you only had to simulate a fraction of it — without losing critical insights? This is exactly where symmetry detection makes a difference. Many biological macromolecular assemblies…