OneAngstrom – Page 162

Stop Misaligned Molecules: A Simple Way to Orient Fragments in SAMSON

One common challenge in molecular modeling is aligning molecular fragments precisely — especially when assembling large systems. Misoriented fragments can lead to structural clashes and inaccurate simulations. If you’ve ever found yourself frustrated by overlapping atoms or spent too much…

Quickly Select Molecular Segments by Atom Counts, Charges, and More

OneAngstrom

When working with complex molecular models, navigating and filtering through large systems can become a challenge. If you are dealing with sizable biomolecules or hybrid materials in SAMSON, you’ve probably found yourself wanting to quickly isolate key parts of a…

Which Symmetry Group Should You Trust?

OneAngstrom

Many molecular modelers working with large biological assemblies—such as viral capsids or homo-oligomeric protein complexes—find themselves asking the same question: What is the correct symmetry group governing my system? This is a common challenge, especially when automatic symmetry detection tools…

Need to Export Molecular Models Easily? Here’s How SAMSON Helps

OneAngstrom

Molecular modelers and computational chemists often face a common hurdle: exporting structures and visualizations in the right format for collaborators, publications, or simulations. With diverse tools requiring specific file formats like PDB, XYZ, CIF, or proprietary types, manually converting and…

When Symmetry Auto-Detection Isn’t Enough: How to Select Your Own Group in SAMSON

OneAngstrom

If you work with large biological assemblies, you’ve likely wondered how to make symmetry work in your favor. Automatic symmetry detection tools can analyze complex structures and identify repeating motifs—saving time when setting up simulations or designing new mutations. But…

A Practical Way to Improve Ligand Unbinding Simulations with P-NEB

OneAngstrom

When simulating molecular transitions, one of the most common challenges is identifying realistic paths between two conformations of a system—especially in cases like ligand unbinding from a protein. Often, modelers generate intermediate structures manually or via linear interpolation, but these…

Keeping Views Consistent in Molecular Animations: How to Use ‘Hold Camera’ in SAMSON

OneAngstrom

Anyone creating molecular animations knows how challenging it can be to maintain a consistent camera view across frames. You might align the perfect visual at frame 10, only to find it slightly shifted by frame 30—just enough to lose coherence…

Design Smarter: How to Create and Use Monomer Sequences in SAMSON

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Designing polymers can be a repetitive task — literally. If you’ve ever needed to build a long polymer with a specific repeating pattern, manually connecting monomers one by one can quickly become frustrating and error-prone. Whether you’re modeling materials or…

Why the Shape of Your Simulation Box Matters More Than You Think

OneAngstrom

When setting up a molecular dynamics simulation, choosing the right boundary conditions can significantly influence both accuracy and performance. One key, yet often overlooked, aspect is the shape of the unit cell used for periodic boundary conditions. By default, many…

Easier Molecular Path Replay—In Reverse

OneAngstrom

For molecular modelers, visualizing conformational changes, docking simulations, or reaction mechanisms using trajectories is part of the daily routine. But what if you need to replay a molecular pathway—accurately—in reverse? Whether you’re trying to demonstrate molecular unbinding, study pathway reversibility,…