OneAngstrom – Page 238

Managing Multiple Molecular Projects in SAMSON: Switching Between Open Documents with Ease

Molecular modelers often work on multiple structures simultaneously—preparing systems, analyzing interactions, or designing new molecules. But managing these workflows effectively can be challenging. You might find yourself juggling several PDBs and simulations, switching back and forth between them to cross-reference…

Finding Charged Structural Groups in Large Molecular Systems

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When working with large molecular systems, molecular modelers often need to isolate relevant substructures for visualization, editing, or simulation. One common task is identifying substructures with specific formal charges—whether to locate reactive sites, predict ion binding regions, or prepare input…

Create and Preview Molecular Animations in SAMSON with the Animator

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Molecular modelers often need more than static visualizations to communicate complex structural changes, docking processes, or dynamic behaviors. Animations and interactive presentations can significantly enhance clarity, whether you’re prepping material for a talk or sharing insights with a broader audience.…

Choosing the Right Unit Cell Shape Can Save You CPU Time

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When setting up molecular simulations, especially for solvated macromolecules, an often-overlooked yet crucial detail is the shape of the unit cell. If you’re a molecular modeler working with periodic boundary conditions (PBC), the choice of cell shape can make a…

Docking Made Simple: Animating Molecular Binding in SAMSON

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Visualizing molecular docking is an essential part of many presentations in molecular modeling. Whether you’re showing how a ligand fits into a protein binding site, or preparing a video to share with collaborators or students, the process of creating smooth,…

Better Molecular Storytelling with Background Transitions in SAMSON

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When presenting molecular models, small visual tweaks can make a big difference. One of the common challenges for molecular modelers is helping audiences stay focused on the scientific message instead of being distracted by inconsistent or harsh visual transitions. That’s…

Stop Guessing: How to Confidently Edit Multiple Atoms in SAMSON

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Edit a group of atoms confidently without breaking their internal structure? If you’re modeling or modifying molecular systems in SAMSON, this question is probably familiar. Precise control over atom positioning can be tricky, especially when you’re dealing with groups rather…

Break Down Complex Molecular Animations into Slides with the Stop Animation

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When presenting molecular dynamics, structural models, or reaction mechanisms, clarity often depends on timing. If your animations move too quickly or lack clear pauses, your audience might miss key points. Fortunately, SAMSON provides a simple but highly effective feature to…

A Simple Way to Animate Molecular Docking in SAMSON

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A frequent challenge in molecular modeling is clearly conveying how molecules interact—especially when it comes to docking. Static images can’t capture the nuances of molecular movement, and scripting animations manually can be time-consuming and unintuitive. If you’ve ever wanted a…

Controlling Bond Types Between Monomers in SAMSON’s Polymer Builder

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When designing synthetic or biopolymers, having precise control over the bond types between monomers is often critical — not just for chemical accuracy, but also for predicting properties like stability, flexibility, or conductivity in downstream simulations. SAMSON’s Polymer Builder extension…