OneAngstrom – Page 53

How to Find the Right Pattern to Modify in Your Molecule

One of the challenges molecular modelers often face when exploring chemical space is deciding where to modify a molecule. Minimal changes at the right location can significantly influence a molecule’s properties—whether you’re optimizing binding affinity, altering pharmacokinetics, or reducing toxicity.…

Switch Views Instantly with Multiple Cameras in SAMSON

OneAngstrom

When working on complex molecular systems, navigating between different spatial regions, projections, or zoom levels becomes a frequent task. Whether you’re analyzing a protein pocket in close detail or comparing macromolecular quaternary structures, this back-and-forth can be tedious and time-consuming.…

A Simple Way to Filter Render Presets in SAMSON Using NSL

OneAngstrom

In molecular modeling, visual fidelity is often more than aesthetics—it’s a way to focus on what really matters. Whether you’re refining a protein surface or comparing molecular contributions in different environments, render presets help you design visual styles quickly and…

Mistake in Your Molecular Model? Use History to Go Back With Precision

OneAngstrom

When modeling complex molecular systems, it’s easy to take one step too many — a misplaced atom, an unintended bond, or even unintentionally overriding valuable data while trying to perfect your structure or simulation setup. The challenge? Rebuilding what you…

Saving Time with Ligand-Based Binding Site Definition in SAMSON

OneAngstrom

Defining the binding site in protein-ligand docking is one of the most crucial — and sometimes tedious — steps in early-stage molecular modeling. If you’re working with a protein structure that already includes a bound ligand, you might wonder why…

From Default to Publication-Ready: Using Visual Presets in SAMSON to Enhance Molecular Visualizations

OneAngstrom

Starting a new molecular modeling project often means spending a lot of time tweaking visual representation settings. If you’ve ever wished there was a way to accelerate this part of your workflow while still producing high-quality, beautiful images, visual presets…

How to Superimpose Two Hemoglobins Without a Script

OneAngstrom

Superimposing protein structures to compare their folds or map conserved regions is a common task in computational biology. But doing it manually—whether with PyMOL scripts or rigid RMSD calculations—can be repetitive and error-prone. If you’re spending time writing custom scripts…

Quickly Find and Filter Property Model Attributes in SAMSON with NSL

OneAngstrom

When working with complex molecular systems in SAMSON, it can quickly become challenging to identify and filter specific components, especially when models grow in size. Whether you’re preparing a dataset for analysis, working on visualizations, or trying to isolate a…

Before You Interpolate: Cleaning Up PDB Structures in SAMSON

OneAngstrom

Generating realistic transition paths between protein conformations is valuable for structural analysis, molecular dynamics, and free energy calculations. However, a common, often frustrating hurdle in these workflows is preparing protein structures: missing atoms, extra chains, water molecules, and ligands can…

Avoid Email Chaos: Send Your Molecular Models the Right Way

OneAngstrom

Many molecular modelers find themselves endlessly emailing large project files back and forth with colleagues. With multiple versions circulating and storage tools that aren’t tailored for research data, things can get convoluted quickly. Who has the latest version? Where did…