OneAngstrom – Page 137

A Clearer Start: Making Molecular Models Appear Smoothly

For molecular modelers and structural biologists working with complex molecular systems, presenting molecules in a clear and digestible way can be a real challenge—especially when you’re trying to guide an audience through a process, a mechanism, or a sequence of…

Filtering Molecules by Partial Charge: A Time-Saving Tip in SAMSON

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When working with complex molecular systems, identifying molecular fragments or structural groups with specific electrostatic properties can be a crucial step — whether you’re designing new molecules, setting up simulations, or analyzing charge distributions. This becomes especially relevant when you…

Working on Just One Molecule? Here’s How to Minimize Precisely in SAMSON

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If you’re modeling molecular systems with multiple molecules, you’ve probably encountered this issue: you want to fine-tune a single molecule or part of it without affecting the rest of your system. Maybe you’re adjusting a ligand conformation in a protein-ligand…

Set Your View in Molecular Videos: Using Hold Camera in SAMSON

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If you’ve ever created molecular presentations or movies, you’ve likely encountered this common issue: your molecules look exactly right in one frame and completely off in the next. This is especially true when animations are missing camera transitions or your…

Tired of Preparing Protein Structures One by One?

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If you’ve ever handled multiple PDB files, you know the pain of preparing them one at a time before a molecular modeling workflow. Manually opening each structure, checking for alternate locations, removing waters or ions, and adding hydrogens can easily…

Making Your Molecular Trajectories Play in Reverse

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One frequent challenge in molecular modeling is effectively visualizing and communicating the motions of molecules. Whether you’re studying a ligand as it exits a binding site or analyzing a protein conformational pathway, being able to show a trajectory in reverse…

A Gentle Rock for Attention: Subtle Dynamics in Molecular Presentations

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When preparing molecular presentations, clarity and subtle focus cues often make the difference between a compelling visual and a confusing one. Among the animation tools available in SAMSON, the Rock animation offers a simple yet effective way to highlight dynamic…

Quickly select molecular paths by number of atoms in SAMSON

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When exploring or comparing molecular conformations, one common challenge modelers face is identifying specific types of paths—especially based on their complexity or size. For instance, locating paths that include a large number of atoms can help identify long chains, extended…

Stuck Exporting Molecular Data? Here’s What You Can Do in SAMSON

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Whether you’re preparing a structure for simulation, sharing results with colleagues, or archiving your research, exporting molecular content is a routine — yet sometimes frustrating — part of computational modeling. Choosing the right format among PDB, XYZ, CIF, and others,…

Make Atoms Appear and Vanish in a Snap: Introducing the Flash Animation in SAMSON

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When preparing molecular presentations or scientific animations, showing and hiding model components at the right moment can make all the difference. Whether you’re revealing specific binding sites, highlighting interactions, or walking through conformational changes, timing is essential. For many molecular…