SAMSON Blog – Page 68

Making Molecular Models Easier to Read with Shadows

When visualizing molecular systems, researchers often struggle with a surprisingly common challenge: understanding how different parts of a structure relate to each other in space. Despite complex 3D views, depth and spatial separation can remain ambiguous—especially in crowded systems. That’s…

Quickly Find Your Favorite Camera Views in SAMSON with Attribute Filtering

OneAngstrom

When exploring complex molecular systems in 3D using SAMSON, users often define multiple camera views: top-down, specific atom neighborhood, or tailored renderings for publication figures. As these views accumulate in a project, a common challenge arises: how to quickly find…

Quickly Find the Camera Nodes You Need in Complex Molecular Models

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When working on molecular design projects, especially when collaborating with large teams or managing complex systems, molecular modelers often deal with a variety of views and camera nodes. Navigating through dozens or even hundreds of them just to focus on…

Quickly Filter Molecular Paths by Atom Counts in SAMSON

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Molecular modelers often work with large and complex structures consisting of multiple paths or conformations. When analyzing such data, one common task is to identify and isolate specific molecular paths based on their size — for instance, focusing on paths…

Choosing the Right Color Palette for Molecular Visualization in SAMSON

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Color is more than just a matter of aesthetics when it comes to molecular modeling. A good color palette can provide insight into structural and chemical properties, helping researchers interpret their data faster and more accurately. On the other hand,…

Efficiently Select Atoms and Residues with Smart Proximity Queries in SAMSON

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Working with complex molecular systems often means handling thousands, even millions of atoms, residues, chains, and other entities. For molecular modelers, selecting specific parts of a model—like all oxygens within a certain range from a binding site—is a common but…

How to Edit Molecular Properties Without Breaking Relationships

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One of the recurring challenges when working with complex molecular systems is the precise editing of atomic or structural properties without disrupting the relationships between nodes. For example, what happens if you want to change the position of a group…

Quickly Find the Right Molecular Folders Using NSL in SAMSON

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When working with complex molecular systems, an increasingly common pain point among modelers is navigating through large data collections to find specific subsets of structures. Whether you’re analyzing protein complexes, supramolecular assemblies, or atomic simulations, you may often need to…

Avoiding Common Pitfalls When Adding Ions to Coarse-Grained Systems in GROMACS Wizard

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One of the subtle yet critical steps when setting up molecular dynamics (MD) simulations with coarse-grained (CG) models is ion addition. If not handled properly, the system can become unbalanced or lead to non-physical behavior during simulation. Fortunately, the GROMACS…

Editing Molecular Dynamics Parameters in SAMSON Without Breaking Your Workflow

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Simulation parameters can make or break the success of a molecular dynamics (MD) run. Whether you’re doing energy minimization or running production simulations, getting those .mdp settings just right is essential. But if you’ve ever spent time tweaking GROMACS parameter…