SAMSON Blog – Page 37

Saving Molecular Flexibility: How to Export Conformations and Trajectories in SAMSON

One of the challenges many molecular modelers face when analyzing the flexibility and dynamics of biomolecules is keeping track of interesting conformations or motion trajectories. Whether you’re preparing a figure for publication, comparing several states of your molecule, or simply…

A Simple Way to Surround Your Protein with Lipids in SAMSON

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Adding lipid layers around proteins is a common requirement in molecular modeling, especially for studying membrane proteins and receptor dynamics. But the process often feels unintuitive, involving multiple software tools, scripts, and tedious alignment steps. If you’ve ever struggled to…

When (and Why) to Minimize Ligands Before Docking

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One common hurdle in molecular docking is dealing with ligand libraries pulled from various sources. Some are fully prepared, others are in 2D or have improper geometries. If docking fails or gives poor results, it’s easy to blame the algorithm…

Smooth Transitions for Molecular Presentations: Using Background Interpolations in SAMSON

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Molecular modelers often face an overlooked but impactful challenge when creating scientific presentations: how to build smooth visual transitions that highlight what matters without distractions. While molecular animations and labels get most of the attention, the background can become a…

Working with Multiple PDB Files? Here’s How to Clean Them All at Once

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If you’ve ever worked with multiple protein structures—for example, when analyzing a protein family, running virtual screening, or preparing data sets for machine learning—you know how tedious it can be to clean and prepare each file manually. Removing solvents, fixing…

Filter and Find Node Groups in Your Molecular Models with Precision

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When working on complex molecular models, locating specific groups of atoms or molecules quickly can save precious time and effort. Whether you’re setting up a simulation, cleaning up a scene, or preparing a figure for publication, repetitive clicking through hierarchical…

A Simple Way to Control Fragment Orientation in Your Molecular Models

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When building molecular systems in SAMSON, many molecular modelers encounter the same challenge: how to precisely control the positioning and orientation of fragments when assembling complex molecules. Whether you’re bonding ligands to a central atom or assembling repeat units in…

A Smoother Perspective: Vertical Camera Transitions with Pedestal Animation in SAMSON

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When preparing molecular animations for presentations, publications, or educational content, achieving smooth and controlled camera movements is essential. A common challenge many molecular modelers face is aligning camera motion with the structure’s spatial dimensions—especially in the vertical direction. This is…

Managing Multiple Molecules? Use SAMSON Documents and Folders Effectively

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When working on complex molecular modeling projects, juggling multiple molecules, simulations, scripts, and views can quickly become overwhelming. A common pain among molecular modelers is managing large projects that involve many interconnected parts. Small mistakes in organization can lead to…

Quickly Hide or Filter Notes in SAMSON with Attribute Flags

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When working with complex molecular systems in SAMSON, it’s common to annotate structures using notes. These notes help document assumptions, highlight areas for further study, or simply organize thoughts directly within the visual model. However, as a project grows, the…