OneAngstrom – Page 200

Visualizing Ligand Unbinding Paths with Energy Curves in SAMSON

Understanding how a ligand dissociates from a protein binding pocket is a key question in many areas of molecular modeling and drug design. Once you’ve found potential unbinding paths, the next practical challenge is making sense of them—where does the…

A Closer Look at the Sequence View in SAMSON: Why It Can Save You Time

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For structural biologists and molecular modelers, the frustration of navigating complex macromolecular systems is all too familiar. You often know the residue or chain you need to focus on—but shifting through a crowded 3D visualization can be tedious and inefficient.…

Write and Run Molecular Scripts Directly in SAMSON’s Code Editor

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When working on complex molecular modeling tasks, Python scripting can save hours of repetitive work. However, switching between external editors, terminals, and visualization platforms often breaks your workflow and makes it harder to test and debug scripts on the fly.…

Easily Managing What You See (and Don’t See) in Property Model Nodes

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One of the common challenges molecular modelers face is managing complex scenes filled with numerous nodes — atoms, molecules, property models, and materials. A cluttered viewport can slow down analysis, impact rendering performance, and simply make it harder to focus.…

Avoid setup mistakes: how GROMACS Wizard auto-assigns the MARTINI force field

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When preparing coarse-grained (CG) molecular dynamics simulations with the MARTINI force field, many modelers spend time double-checking whether they’ve configured the correct parameters and files. One small but frequent pitfall is using a CG topology—often from Martinize2—but forgetting to assign…

Turning Molecular Presentations into Slides: A Simple Way to Pause Animations

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When presenting a molecular simulation or model to an audience, timing is everything. You may want to highlight a key step in a mechanism, pause for discussion, or transition smoothly between ‘slides’ of your demonstration. But how do you break…

Can’t Save Your Molecular Model the Way You Want? Meet SAMSON Exporters

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One of the most common frustrations molecular modelers face is being unable to save their work in the right format. Whether you’re preparing to submit a structure to a database, running simulations in an external program, or simply sharing an…

Quickly Generate Analogs by Replacing Atoms with the SMILES Manager

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Exploring how small changes in your molecules impact their behavior is a key activity in molecular modeling, especially during hit expansion or lead optimization. But trying out dozens of variations by hand? That gets tedious quickly. This is where the…

Progressive Disappearance: A Cleaner Way to Show Molecular Changes

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When preparing molecular animations, it can be tricky to control how atoms appear and disappear without overwhelming your audience. In many visualization tools, fading atoms using transparency can cause visual clutter, making it hard to follow the structural changes you…

Creating Custom Index Groups During Equilibration or Simulation in GROMACS Wizard

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When working on molecular dynamics simulations with GROMACS, one of the recurring challenges is managing custom index groups. These groups are often necessary for tasks like defining pull groups, analyzing specific parts of your system, or applying targeted constraints. While…