SAMSON Blog – Page 577

When (and Why) to Minimize Ligands Before Docking

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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

OneAngstrom

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…

Quick Groups in SAMSON: Save and Recall Your Molecular Selections Instantly

OneAngstrom

In molecular modeling, repetitive selection of the same atoms, residues, or fragments can quickly become tedious—especially when dealing with complex biomolecular systems. Whether you’re analyzing ligand binding sites, highlighting functional groups, or toggling between different molecular regions, having to re-select…

Using External Tools in Molecular Modeling with SAMSON Apps

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For many molecular modelers, one persistent challenge is integrating external tools — whether they’re command-line executables, web services, or in-house scripts — into a unified modeling workflow. Repeatedly shifting data between programs, converting formats, and writing glue code to link…