SAMSON Blog – Page 58

What File Formats Does SAMSON Support, and Why Does It Matter?

When you’re working with molecular modeling software, one of the first real bottlenecks you might hit is file format compatibility. It often shows up when you try loading a structure you just downloaded from a public database—or even when trying…

Avoiding Common Pitfalls When Setting Ligand Atoms in Unbinding Pathway Simulations

OneAngstrom

If you’ve ever tried to simulate ligand unbinding pathways from proteins, then you’ve likely faced the challenge of defining which atoms belong to the ligand — especially in systems containing cofactors, solvent molecules, or multiple ligands. Making a mistake at…

Effortlessly Track Atomic Motion in Your Presentations

OneAngstrom

When creating molecular animations or presentations, one of the recurring challenges for modelers is capturing the motion of atoms over time. Whether you’re simulating binding events, assembly steps, or conformational changes, showcasing how atoms move is essential—and being able to…

Clean Dozens of Protein Files in Seconds with Batch Protein Prepare

OneAngstrom

Preparing a single protein structure for simulations is already a multi-step process. If you’ve ever had to do that with dozens or hundreds of PDB files, you’ve probably felt the pain of repetitive cleanup: removing unwanted molecules, adding missing atoms…

Efficiently Target Residues in Molecular Models with Smart Tagging

OneAngstrom

When working with complex biomolecular structures, one of the most common tasks is selecting specific residues based on properties like charge, polarity, backbone completeness, or location within the secondary structure. This need arises in countless scenarios: analyzing binding pockets, preparing…

Understanding Visual Models in SAMSON: What They Are and How to Use Them

OneAngstrom

When working with molecular systems, the way data is visualized often makes a huge difference in understanding structure and function. A common challenge among molecular modelers is navigating the visual complexity of nanosystems without getting overwhelmed or missing crucial insights.…

Visualizing Molecular Trajectories with the Record Path Animation in SAMSON

OneAngstrom

In molecular modeling and simulations, it’s often essential not only to compute how particles move but also to clearly visualize the trajectory they follow. Whether you’re simulating protein-ligand interactions, assembling complex systems, or simply preparing a presentation, being able to…

Preview and Create Symmetric Protein Replicas with Ease

OneAngstrom

When working with protein structures, it’s common to begin with asymmetric units from the Protein Data Bank (PDB). However, research and design tasks like analyzing quaternary structures, identifying protein-protein interfaces, or building full biological assemblies often require the generation of…

Creating Coarse-Grained Models for Multiple Protein Replicas in SAMSON

OneAngstrom

In many molecular simulations, especially when studying aggregation, crowding, or system size effects, researchers need to work with several replicas of the same protein. However, preparing these multi-replica systems for coarse-grained (CG) simulations can be a tedious and error-prone process—especially…

Saving Molecular Snapshots Made Easy: A Look at Capture Preferences in SAMSON

OneAngstrom

When you finally get that perfect view of your molecular model — maybe a key binding pocket, an optimized ligand pose, or a nicely minimized structure — you probably want to save it as a high-quality image. But the default…