SAMSON Blog – Page 352

How to Quickly Find Hidden or Visible Nodes in Molecular Scenes

When working on large molecular models, it becomes increasingly important to manage visibility efficiently. You might be focused on just one part of the structure — a ligand binding site, a water shell, or a specific chain. But if hidden…

Efficiently Filter Charged Residues in SAMSON with NSL

OneAngstrom

When working on protein modeling workflows, one of the recurring tasks is identifying and selecting residues based on their electrical charge. Whether you’re optimizing electrostatic interactions, analyzing salt bridges, or preparing electrostatics-related simulations, filtering charged amino acids is a crucial…

A Step-by-Step Guide to Building Custom Molecules Atom by Atom in SAMSON

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Molecular modelers frequently need to construct specific chemical structures not readily available in molecular libraries. Whether you’re reproducing a model from a journal article or exploring new chemical scaffolds, building molecules atom by atom is often a key part of…

Easier Custom Atom Selection in GROMACS Simulations with SAMSON

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Many molecular modelers using GROMACS have run into this: you want to track or manipulate a specific set of atoms during a simulation—maybe the side chains of neutral amino acids or every non-C-alpha atom in a protein. But GROMACS only…

Quickly Find Structural Groups by Atom Count in Your Models

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When building or analyzing large molecular systems, it can be a challenge to identify specific structural groups of interest — especially when dealing with hundreds or even thousands of groups. What if you want to isolate only those groups with…

Running GROMACS in the Background: How to Monitor Local Simulations with Ease

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When running molecular dynamics (MD) simulations, especially those that take time to compute, a common frustration among molecular modelers is not being able to track progress easily without interrupting their workflow. Whether you’re testing new force field parameters, prepping simulations…

Easily Select Visual Representations in SAMSON Using NSL

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A common task in molecular modeling involves managing the many visual representations of structures—especially when the scene includes numerous models like ball-and-stick, ribbon, or surface renderings. Being able to quickly isolate, hide, or modify these visual elements is essential for…

Working Late? Make Molecular Modeling Easier on Your Eyes with Dark Mode

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Many molecular modelers spend hours working with intricate structures, adjusting render settings, and preparing visuals for publications or presentations. If you’re someone who often finds yourself working in dim lighting or during evening hours, you’ve likely experienced some discomfort from…

Why Your Molecular Labels Look Off — And How to Fix It

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Labels are a critical part of molecular visualization — they help identify atoms, residues, molecules, and key spatial measurements. But if you’re a molecular modeler working in SAMSON and your Viewport looks cluttered or unclear, misaligned labels might be the…

Avoid This Common Mistake When Setting Up Protein Transitions

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One of the most frequent issues faced when interpolating between protein conformations is something many don’t anticipate: disconnected molecular structures. If you’ve ever encountered the error message “Cannot proceed because the structure does not make one connected component” while using…