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A Practical Guide to Setting Up Interactive Simulations in SAMSON

If you’ve ever wanted to adjust molecular geometries while watching energies and forces respond in real-time, SAMSON‘s interactive simulations offer an intuitive way to do so. But if you’ve never added a simulator before, the process can seem a bit…

Quickly Find the Chains You’re Looking For with NSL

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Anyone working with complex molecular models knows how quickly a project can become overwhelming. Once you have large protein structures, assemblies, or entire molecular systems with multiple chains, managing and navigating them effectively becomes a challenge. What if you’re only…

When a Molecule Just Won’t Stick: Automating Atom Undocking in SAMSON

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If you’ve ever prepared molecular animations for presentations, publications, or educational content, you know how time-consuming it can be to manually simulate atoms or molecular groups moving away from their binding sites. Whether you’re modeling a drug molecule departing from…

Avoid Frustration When Working with Multiple Protein Conformations: A Quick Guide

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When modeling protein transitions — for instance, switching between open and closed conformations — a surprisingly common obstacle is just getting the input right. If your two conformations come in separate PDB files, you might scramble to align and manage…

Comparing Protein Sequences in 3D: A Practical Guide in SAMSON

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When comparing proteins across species, variants, or conditions, sequence alignment is often the first step. But for molecular modelers, aligning only sequences may not capture the impact of structural context — and that’s where SAMSON’s Protein Aligner becomes especially helpful.…

Making your molecular models clearer with visibility flags

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In molecular modeling, clarity is essential. When working with complex assemblies, it’s easy for molecular scenes to become visually overwhelming. SAMSON’s Node Specification Language (NSL) provides a simple way to control the visibility of elements using note attributes. This is…

Avoiding Force Field Frustration: Efficiently Setting Up UFF in SAMSON

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Setting up a molecular simulation can sometimes feel like a road paved with pitfalls—especially when it comes to selecting and initializing a force field. For many researchers, the Universal Force Field (UFF) offers the convenience of broad coverage and applicability,…

Don’t Let Your Molecular Labels Get Lost: Fine-Tune Visibility and Fonts in SAMSON

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When working on complex molecular systems, clarity is key. Whether you’re presenting a structure in a paper, discussing a finding with a colleague, or simply trying to make sense of your own model, labels help bring order to atoms, residues,…

Smooth Sideways Camera Movements for Molecular Presentations: The Truck Camera Animation

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If you’ve ever tried to capture smooth horizontal motion in your molecular animations — like sliding across a membrane or tracking a large biomolecular structure — you’ve likely found it challenging to keep both the focus and framing consistent. Shaky…

What Does ‘Visible’ Really Mean in Molecular Animations?

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When dealing with complex molecular systems, managing visibility can quickly become a headache. Whether you’re inspecting protein motions, visualizing ligand movements, or preparing animations for presentations, knowing exactly which nodes are visible (and why) is essential. Confusingly, SAMSON animation nodes…