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Cleaning Hundreds of PDBs Without Scripting: Protein Batch Preparation in SAMSON

If you’ve ever worked with multiple protein structures from the Protein Data Bank (PDB), you’ve probably experienced the repetitive – and tedious – process of cleaning them: stripped waters, removed alternate locations, deleted ligands, added missing hydrogens… the list goes…

Creating Custom Index Groups in GROMACS with SAMSON

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When setting up molecular dynamics simulations in GROMACS, it’s often useful—if not essential—to define specific groups of atoms for analysis and specialized operations (e.g., as pull groups or monitoring specific domains). These are known as index groups. While GROMACS can…

Disassemble Molecular Structures Without Manual Tweaking

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When presenting complex molecular assemblies, it’s often helpful to clearly show how components fit together. But how do you break apart a molecular complex in a clean, controlled way—without moving every atom manually? This is where the Disassemble animation in…

Quickly Find Molecules with Specific Structural Features in SAMSON

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When working with large and complex molecular systems, it’s easy to feel overwhelmed trying to locate structures of interest. Whether you’re screening databases, comparing different models, or cleaning up PDB data, quickly filtering molecules based on specific attributes can save…

Exporting Molecular Models from SAMSON: What You Need to Know

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One of the most common pain points for molecular modelers is getting their data—atomic and structural information, visualizations, and simulation results—out of their modeling platform in a usable format. Whether you’re sharing your research, preparing input for a simulation engine,…

See Your Molecules Clearly: How SAMSON’s Visual Models Can Streamline Your Workflow

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Molecular modelers often spend a significant amount of time trying to fine-tune how molecular structures are displayed. Whether it’s for better analysis, clearer presentations, or publication-ready visuals, there’s a constant need to control how nanosystems are represented graphically. In SAMSON,…

Progressive Disappearance in Molecular Models: A Clearer Way to Present Complex Structures

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When preparing molecular animations for presentations or publications, clarity and focus are essential. One of the common challenges molecular modelers face is how to gently de-emphasize or hide specific parts of a model without abruptly removing them. A sudden disappearance…

When Less is More: Concealing Atoms to Clarify Molecular Mechanisms

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Complex molecular structures often overwhelm audiences when presenting biochemical mechanisms or molecular simulations. Showing every atom and bond might be accurate, but it quickly becomes counterproductive if the viewer can’t follow what’s happening. This is a challenge many molecular modelers…

Avoiding Input Errors in GROMACS Equilibration: A Quick Guide to Selecting Structures

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If you’ve ever run into issues at the start of an equilibration step in GROMACS, you know how frustrating it can be to realize that the problem was simply an incorrect input file path or format. This is particularly common…

Making Fragments Fit: A Closer Look at Orienting Molecular Fragments in SAMSON

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When building complex molecular models, one of the recurring challenges is aligning functional groups or fragments precisely and efficiently. Incorrect orientation can result in steric clashes, unrealistic geometries, or simply more work adjusting everything afterwards. If you’ve ever tried rotating…