OneAngstrom – Page 144

Why Your SAMSON Extensions May Not Load—and How to Make Sure They Do

If you’ve ever launched SAMSON and found that one of your favorite Extensions wasn’t loaded, even though it worked last week, you’re not alone. Molecular modelers relying on Extensions for simulations, visualizations, or custom tools may sometimes encounter this frustration.…

Cleaning Protein Structures Before Docking: Why It Matters and How to Do It in SAMSON

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If you’ve ever tried protein-protein docking and encountered strange results — unexpected clashes, misaligned complexes, or long computation times — chances are your system wasn’t properly prepared. Protein preparation is foundational for successful docking, yet it’s often overlooked or done…

Fine-tuning Molecular Visuals with Custom Color Palettes in SAMSON

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Color is an essential tool for molecular modelers. Whether you’re communicating structural insights, visualizing properties like hydrophobicity or temperature factors, or simply enhancing the aesthetic clarity of a molecular scene, choosing the right color scheme makes a big difference. But…

Using Python Scripts with SAMSON: A Quick Guide for Molecular Modelers

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Molecular modelers increasingly rely on scripting to streamline repetitive tasks, automate analyses, or create custom simulations. If you use Python in your workflow, integrating scripts directly into your modeling environment can dramatically reduce friction and time. SAMSON, the integrative platform…

Skip the Repeats: Simulating Only the Asymmetric Unit in Large Protein Complexes

OneAngstrom

Molecular modelers working with large symmetric assemblies—like viral capsids or multi-subunit protein complexes—often face a dilemma: Should I simulate the entire structure, or is there a smarter way? In many cases, the repetitive nature of these biological assemblies means you’re…

Prevent Docking Failures: Manual Ligand Preparation for Covalent Docking

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When performing covalent docking, one of the most common sources of error stems from improper ligand preparation — especially when working with ligands already covalently bound in crystal structures. By default, automatic preparation tools may fail to reconstruct the originally…

Tired of cluttered views? Control label visibility in SAMSON with precision.

OneAngstrom

One of the most common frustrations in molecular modeling is visual clutter. As molecular systems grow in complexity, the accumulation of labels—whether for atoms, residues, or custom annotations—can quickly become overwhelming. This doesn’t just make visualization harder, it can also…

Exporting Ligand Trajectories for Free Energy Calculations

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One of the most common setup pains in molecular modeling arises when preparing atomic coordinates along a ligand’s exit or binding path. Whether you’re running free energy calculations, benchmarking enhanced sampling methods, or analyzing transition mechanisms, a clean and flexible…

Getting Precise with Pause: Better Control Your Molecular Presentations

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Creating compelling molecular animations often requires more than just smooth transitions and camera movements. Sometimes, you need to pause and let your audience absorb a key concept or molecular interaction—especially in educational content or when presenting complex conformational changes. Fortunately,…

Quickly Find Molecule Paths by Atom Count in SAMSON

OneAngstrom

When working with large molecular systems in SAMSON, it’s very common to work with conformation paths. Whether you’re navigating different states of a trajectory or trying to prepare a dataset for analysis, one common challenge is identifying only those paths…