SAMSON Blog – Page 151

When Your Molecular Model Goes Sideways: Meet the History View

If you’ve ever clicked a button in your molecular modeling process and instantly regretted it, you’re not alone. Trial and error is part of any design process, but in molecular modeling, mistakes can be costly—in time, in effort, and in…

How to Color-Code Distances and Angles in Your Molecular Models

OneAngstrom

When working on complex molecular models, visual clarity can make all the difference. If your structures are crowded with overlapping labels and measurements, it becomes harder to analyze your data, communicate your findings, or even stay focused. Fortunately, SAMSON provides…

Why Understanding Bond Types in NSL Can Save You Hours of Headache

OneAngstrom

If you’ve ever spent time sifting through complex molecular models, trying to isolate specific interaction types, you know how tricky it can be to filter out exactly what matters. Whether it’s identifying aromatic systems, differentiating single and double bonds, or…

Why Molecular Colors Matter More Than You Think

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For molecular modelers, data visualization is not just aesthetic—it’s functional. The way atoms, residues, and molecules are colored can directly impact the clarity of your interpretations, the speed of your decision-making, and even the persuasiveness of your publications or presentations.…

Building Custom GROMACS Index Groups without the Guesswork

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When working with large biomolecular systems using GROMACS, it’s often necessary to define custom index groups—for example, to specify pull groups for umbrella sampling, analyze specific subsets of atoms, or apply restraints. But creating these groups manually using gmx make_ndx…

Control what you see: making sense of label visibility in SAMSON

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In large molecular models, it’s easy to feel overwhelmed by the sheer number and variety of elements displayed. Labels—while useful—can quickly clutter the view, especially when the model grows in complexity. Turning labels on and off manually for dozens or…

A Smarter Way to Showcase Molecular Motion: Rotating Around the Centroid

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When visualizing molecular systems and presenting dynamics to collaborators, students, or in publications, clarity and focus matter. One subtle yet powerful tool in the molecular modeler’s toolkit is the ability to rotate a selected group of particles around its geometric…

Saving Protein Motions as PDB Trajectories in SAMSON

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One of the challenges structural biologists often face is not only computing and visualizing protein motions, but also saving them in a way that is easy to analyze, compare, or share with collaborators. Whether you’re studying conformational transitions or designing…

From Sequence to Structure: Submitting AlphaFold-2 Predictions in SAMSON

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Predicting protein structures has traditionally been a time-consuming and computationally intensive task. With the rise of deep learning approaches like AlphaFold-2, this process has become more accessible — but still requires a convenient interface and computational resources that not all…

From 3D Mesh to DNA: Building Wireframe Nanostructures with Adenita

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One recurring challenge for researchers and designers working in DNA nanotechnology is building complex molecular wireframe shapes—quickly and correctly. How can we effortlessly transform a 3D mesh into a DNA-based model ready for simulation or experimentation? Adenita, an extension of…