SAMSON Blog – Page 331

Querying Backbone Groups by Atom Counts in SAMSON

Molecular modelers working with complex systems often need to focus on specific subsets of molecules, such as backbone groups with particular atomic compositions. Manually identifying these substructures can be time-consuming and prone to error—especially in large biomolecular systems. Fortunately, the…

Finding Molecular Groups by Partial Charge in SAMSON

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When working with complex molecular systems, understanding how charge is distributed is often key to understanding behavior—especially in systems involving electrostatics, binding interactions, or solvation. One common challenge for molecular modelers is quickly identifying structural groups with specific partial charges.…

When Molecules Take a Spin: Using the Rotate Animation in SAMSON

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Creating compelling molecular presentations can be surprisingly challenging—even for experienced modelers. A common issue arises when trying to showcase structural dynamics or orientation within a molecular system. While static models provide structural information, they often fail to communicate spatial relationships…

Making Molecular Models Breathe: Using the Pulse Animation in SAMSON

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When presenting molecular models, clarity and engagement matter. Static images or rigid transitions can sometimes make it difficult to convey the dynamics of complex molecular assemblies. If you’ve ever struggled to draw attention to specific parts of your molecular model…

Controlling Your Molecular Flythroughs: A Guide to Camera Movement in Presentations

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One of the biggest challenges molecular modelers face when creating visual presentations of their models is how to guide the audience’s attention smoothly — especially when illustrating binding pathways, conformational changes, or transport channels. A static camera angle just doesn’t…

Precise Atom Selection in SAMSON Using Expressions

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Whether you’re preparing a simulation, cleaning up atomic structures, or designing nanoscale materials, selectively hiding, showing, or modifying atoms can be tedious if done manually. SAMSON, the integrative molecular design platform, comes with a powerful toolset that simplifies this process:…

From Invisible to Insightful: Show Molecular Complexity with the Reveal Atoms Animation

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When working with complex molecular models, clarity is essential. Molecular modelers often face the challenge of communicating dynamic processes, stepwise assemblies, or structural differences — and static images or abrupt transitions are rarely effective. If you’ve struggled to make molecular…

When to Show or Hide Labels: A Small Tweak for Cleaner Molecular Models

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In molecular modeling, clarity matters. A cluttered visual representation can easily hide key features of your system. This becomes especially noticeable when labels—used to annotate atoms, residues, or molecules—remain visible at all zoom levels in the model. Thankfully, SAMSON offers…

Need an Older Version of SAMSON? Here’s How to Install It Safely

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In the fast-moving world of software development, updates are inevitable. However, in scientific research, especially molecular modeling workflows, stability and repeatability often matter more than newer features. If your current project depends on a specific functionality from an older version…

How To Avoid File Hunt Fatigue When Equilibrating Your System

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If you’ve spent time preparing a molecular dynamics system for simulation, you’ve probably run into this scenario before: you’re ready to move to the next step, but you can’t remember where your last output file was saved—or what it was…