SAMSON Blog – Page 544

Running AlphaFold-2 Predictions in SAMSON: Simplified Structure Modeling from FASTA Files

Molecular modelers often face a common challenge: how to reliably predict protein structures with tools that are accessible, secure, and flexible enough to support a variety of research workflows. With the growing popularity of AlphaFold-2, the ability to make structure…

Making Molecules Appear When You Want Them To

OneAngstrom

Controlling the visibility of elements in molecular animations can be frustrating. You might want some parts of your model to appear at specific times without gradually fading in or tweaking transparency. This is especially important in presentations or educational videos…

Making Molecules Rock: A Simple Way to Add Motion to Your Molecular Visualizations

OneAngstrom

Visual storytelling is a powerful tool in molecular modeling, whether you’re preparing a research presentation, explaining a mechanism, or highlighting a key structural feature. Molecular animations, when done right, can reveal dynamics that a static image simply can’t capture. However,…

Drawing Nanotubes with a Drag—Fast Design in SAMSON’s Viewport

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Designing carbon nanotube (CNT) structures can be a repetitive chore for molecular modelers and nanoscientists, especially when quick iterations or small variations are needed. Using traditional parameter input forms for each tube can feel cumbersome. But if you’re working in…

A Quick Way to Minimize Entire NMR Ensembles at Once in SAMSON

OneAngstrom

Working with NMR-derived molecular structures often means managing ensembles of conformations. But what if you need to quickly energy-minimize all conformations in one go—without messing with topology files or writing scripts? The Molecular Restrainer extension in SAMSON provides a fast…

Avoid Installation Frustration: SAMSON Doesn’t Require Admin Rights

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Installing complex molecular modeling software can sometimes feel like a project of its own—especially in restricted computing environments like corporate or university networks. One of the common stumbling blocks modelers face is the need for admin rights to install software,…

Tired of Hidden Nodes? How to Easily Select Visible Parts of Your Molecular Model in SAMSON

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It can be frustrating: You import or build a molecular system in SAMSON, and some parts seem to be disappearing, can’t be selected, or just don’t respond the way you expect. In many cases, this comes down to node visibility…

Why You Might Want to Stop and Breathe During Your Molecular Presentation

OneAngstrom

Molecular modelers often spend hours perfecting animations that communicate complex mechanisms and structures with clarity. When showing a ligand docking process or a protein folding simulation, even a few fast-moving frames can disrupt the viewer’s ability to keep up. This…

Freezing Atoms to Minimize Only What Matters

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Interactive molecular minimization in SAMSON is convenient and fast, but what if you’re only interested in minimizing part of a molecule—say, just a few atoms or a flexible side chain—without altering the rest of the structure? When setting up a…

Recording Atomic Movement in Molecular Animations: Efficiently Capture Atom Paths in SAMSON

OneAngstrom

When working on molecular presentations, especially those that involve atomic movements such as docking, assembly, or simulation, demonstrating atom trajectories can significantly improve clarity and understanding. But how do you precisely capture those trajectories for presentations and further analysis? This…