OneAngstrom – Page 134

Choosing the Right Unit Cell Shape Can Save You Simulation Time

Working on a molecular simulation in solution? If the system you’re modeling is approximately spherical—like a protein, micelle, or nanoparticle—you might be wasting compute time without realizing it. Let’s talk about unit cell shapes and how your choice impacts performance…

A Subtle Way to Bring Molecular Models to Life: The Rock Animation

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When creating molecular presentations or educational visualizations, small movements can make a big difference. One recurring challenge molecular modelers face is how to add subtle, dynamic motion to molecular structures in a way that enhances viewer understanding without overwhelming the…

From SMILES to 3D in SAMSON: A Practical Guide for Molecular Modelers

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One of the recurring challenges in cheminformatics and molecular modeling is converting a simple SMILES string into a realistic 3D molecular structure. For many modelers, this means juggling scripts, toolkits, or web services — often repeating the same task across…

Which Molecular File Formats Can You Load Into SAMSON?

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Anyone who has worked with molecular modeling knows the frustration of incompatible file formats. You might receive data in PDB format from a colleague, simulate a system in LAMMPS which outputs a DAT file, or need to visualize a CIF…

Building Your First SAMSON Extension: What You Need to Know

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For many molecular modelers, there’s often a moment when the built-in tools just don’t go far enough. Whether you’re exploring custom simulations, integrating code you’ve already written, or just want to tailor your modeling environment to your workflow—extending your platform…

Quickly Isolate Molecules in Complex Models with Visibility Filters

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If you work with complex molecular systems, you’ve likely faced the challenge of cleaning up crowded views. Structures with hundreds or thousands of molecules can overwhelm your workspace and slow down your workflow. Whether you’re analyzing a protein-ligand interaction or…

Working with Partial Charges in Structural Models: A Quick Guide for Modelers

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When working with molecular models, filtering and querying based on electrostatic properties can be essential for selecting molecules of interest, especially in tasks like charge optimization, molecular docking, or interaction prediction. One commonly used property for this is the partial…

Tired of Reformatting Molecular Data All the Time?

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One of the most persistent difficulties in molecular modeling is the variety of file formats used by different databases, instruments, and software tools. Whether you’re working with PDB files from the Protein Data Bank, volumetric electron density maps, or proprietary…

Stop Wasting Time on Complex Selections: A Quick Guide to NSL in SAMSON

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If you’ve ever spent too long trying to manually select specific atoms, residues, or molecular components for your simulation or visualization, you’re not alone. This is a common challenge among molecular modelers and structural biologists. Fortunately, the Node Specification Language…

Opening Molecular Files Without Hassle: What Formats SAMSON Can Handle

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One of the most common—and often frustrating—challenges in molecular modeling is dealing with incompatible file formats. You’ve got simulations in LAMMPS, models from PDB, trajectories from GROMACS, and maybe some JSON-based DNA origami data for good measure. Ensuring that your…