SAMSON Blog – Page 107

Struggling to Load Your Molecular Data? Here’s How SAMSON Handles It.

Whether you’re visualizing a protein-ligand complex or analyzing cryo-EM data, loading external molecular data is often the very first—and sometimes frustrating—step of your workflow. Inconsistent file formats, unsupported extensions, or partial loading of structures can make this simple task surprisingly…

Running Multiple Molecular Simulations at Once with GROMACS Wizard

OneAngstrom

Setting up molecular dynamics (MD) simulations is often time-consuming, especially when you need to run many initial conformations of the same molecular system. For example, you might want to test different ligand poses, protein conformations, or results from docking, normal…

What’s Really Visible in Your Molecular Model? A Close Look at the `visible` Attribute

OneAngstrom

When working on large and complex molecular systems, one common frustration for molecular modelers is managing visual clarity. Whether designing a nanosystem or analyzing simulation results, ensuring that only the relevant parts of the model are visible can dramatically impact…

Missed a Tool in SAMSON? Here’s How to Make Sure GROMACS Wizard Is Installed

OneAngstrom

For molecular modelers who rely on powerful tools like GROMACS to perform simulations efficiently, it can be frustrating to realize that a crucial extension isn’t installed—or worse, to not even know it’s missing. If you’re using the SAMSON platform, ensuring…

How to Find Atoms Inside a Spatial Region in SAMSON

OneAngstrom

When analyzing or simulating molecular systems, it’s often helpful to focus on a specific part of the structure. Whether you are calculating partial charges, analyzing solvent distribution, or preparing a local environment for docking or QM calculations, selecting atoms in…

Running Python Scripts Inside SAMSON: What You Need to Know

OneAngstrom

If you’re working with molecular modeling and already using SAMSON, you might often find yourself juggling different tools just to run or tweak a Python script. But did you know SAMSON has native support for Python scripting? Whether you’re analyzing…

How to Find Molecules with Complex Substructures Using SMILES Manager

OneAngstrom

Searching for the right molecule in a library can be a slow and frustrating process—especially when you’re dealing with substructures. Maybe you’re designing a compound with a specific functionality, or maybe you want to filter out only the molecules that…

The Quiet Power of Protein System Preparation (And How to Do It Right)

OneAngstrom

Before jumping into docking simulations, there’s one crucial step that experienced molecular modelers know better than to skip: system preparation. While it might feel like a formality, not preparing your protein structures correctly can lead to misleading results or failed…

Temporary or Saved? Mastering Measurement Labels in Molecular Modeling

OneAngstrom

When working on molecular models, measurements are vital. Whether you’re calculating bond lengths, angles, or torsion, clarity and reproducibility are essential — especially when presenting your model, collaborating, or coming back to your work months later. This is where SAMSON’s…

Switch Selections Like a Pro with Quick Groups in SAMSON

OneAngstrom

When working on complex molecular systems, it’s common to repeatedly switch between different selections—ligands, protein pockets, water molecules, and more. But let’s face it: manually selecting the same nodes over and over is time-consuming and error-prone. Fortunately, SAMSON offers a…