OneAngstrom – Page 375

From prompt to Python: writing scripts using natural language in SAMSON

For many molecular modelers, writing Python scripts is a common task—but it can also be a source of friction. Whether you’re building custom visualizations, automating repetitive tasks, or analyzing structural properties, scripting can be both powerful and time-consuming. But what…

Avoid Topology Errors: How to Renumber Chains and Residues in Replicated Protein Systems

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If you’ve ever tried to simulate a system with multiple replicas of the same protein and ran into topology generation errors, you’re not alone. This is a common issue when working with coarse-grained modeling tools like Martinize2 in SAMSON. The…

A Practical Guide to Finding Conformational Paths Between Protein States

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Many molecular modelers face a recurring challenge when studying functional protein dynamics: how to connect two known conformations of a protein—say, an open and a closed state—with a realistic transition path. This is a critical step for gaining insights into…

Quickly Define Custom Atom Groups for GROMACS Simulations in SAMSON

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When setting up a simulation involving custom pulling forces in GROMACS, one of the first roadblocks many molecular modelers face is the creation of appropriate index groups. These groups are essential to define regions of interest in biomolecular simulations—whether you’re…

Quick ways to filter hidden and visible nodes in SAMSON with NSL

OneAngstrom

When working on complex molecular systems in SAMSON, we often deal with a multitude of objects: atoms, groups, models, data nodes, and more. Among these, property models define additional data on molecular systems, such as electrostatic potentials, surface properties, or…

A Simple Way to Visualize Molecular Rotation in Your Animations

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Adding motion to molecular simulations can help communicate structural dynamics and emphasize specific interactions. One common need in molecular modeling is showcasing how a group of atoms or residues rotates in 3D space—whether for presenting conformational changes or emphasizing the…

Switching Views Without Losing Your Spot: Using Multiple Cameras in SAMSON

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When working on complex molecular systems, modelers often need to switch between different spatial views—zoomed-in interactions, overall structure, or specific orientations. However, changing perspective often means losing track of a previously tuned camera view, and manually restoring it can be…

Taming Scenes: How to Identify and Work with Render Presets in SAMSON

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When working on complex molecular models in SAMSON, visual clarity can quickly become a challenge. Whether you’re preparing a scene for publication, for collaboration, or simply managing multiple layers of molecular systems, you may find yourself needing to precisely control…

Quickly Share Molecular Models with Colleagues or Students Using SAMSON Documents

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If you’re working in molecular modeling, you’ve probably been through the painstaking task of sharing files and simulations with collaborators: emailing attachments, using third-party storage platforms, managing access rights manually… not to mention syncing updates across multiple versions of the…

Stop Clicking, Start Searching: Selecting Molecular Structures with NSL

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One of the most common points of friction for molecular modelers is efficiently selecting structures—like ligands, residues, or atoms—from large and complex molecular systems. If you’ve ever spent more time than you’d like manually clicking through molecules to highlight regions…