OneAngstrom – Page 173

Quickly Focus on the Right View: Filtering Cameras in SAMSON with NSL

When working with complex molecular systems in SAMSON, managing multiple cameras—each representing a different molecular view or visualization setup—can easily become overwhelming. Especially in large projects or collaborative environments, a user might find themselves digging through long lists of viewpoint…

Making Molecular Presentations Smoother with Rotate Animations

OneAngstrom

When you prepare molecular animations to explain your research or present your findings, the clarity of visualization often makes the difference between confusion and understanding. A common challenge faced by many molecular modelers is: how to intuitively highlight structural features…

Targeting Specific Node Groups in SAMSON Without the Guesswork

OneAngstrom

When working with complex molecular systems in SAMSON, it’s common to organize nodes into groups to simplify selection and manipulation. Whether you’re modeling biomacromolecules or designing nanosystems, node groups help provide structure. But once your model grows, quickly identifying or…

Focus Without Following: Keeping the Camera Steady in Molecular Animations

OneAngstrom

When creating molecular animations, researchers and educators often want to visualize how specific regions of a molecule or molecular system behave over time. However, a common frustration is trying to keep the camera focused on a particular region without having…

Quickly Show or Hide Notes in Molecular Models with NSL

OneAngstrom

When molecular modelers build and analyze complex systems, they often annotate their models using note nodes. These notes can contain textual information, comments, or metadata that are extremely useful during collaborative work or when reviewing projects later. However, as projects…

Avoid Errors When Modeling Protein Transitions: How to Prepare Conformations for Path Search

OneAngstrom

Preparing protein conformations properly is a necessary step before computing transition paths between them. However, it is often a source of frustration for molecular modelers. Missing atoms, inconsistent residue numbering, or incompatible PDB files can all lead to failed simulations…

Create Your Own Atom Groups in GROMACS Wizard Without Writing Index Files

OneAngstrom

Anyone who’s worked with GROMACS knows how essential index groups are when setting up complex molecular dynamics simulations. Whether you’re pulling a specific domain during umbrella sampling or analyzing RMSD for specific atoms, you typically need to create custom index…

Importing Equilibration Results in GROMACS Wizard Without Losing Your Mind

OneAngstrom

Running molecular dynamics (MD) simulations is just one part of the journey. Once a simulation finishes, many researchers face a more frustrating step: importing and analyzing the results. This is especially true when working with multi-step workflows like those used…

Efficiently Managing Labels in Molecular Models

OneAngstrom

When working with complex molecular models, it’s easy to become overwhelmed by the variety of entities displayed in your workspace. Whether you’re inspecting annotations, distances, or custom text markers, labels are often key to interpretation. But without efficient controls, label…

Synchronizing Trajectories: A Better Way to Play Molecular Paths in SAMSON

OneAngstrom

When working with molecular systems that involve flexible conformations, dynamics, or simulations, visualizing movements across trajectory frames can quickly become unwieldy. Molecular modelers often need to revisit and align transitions—whether from different simulations, conformational states, or interpolation paths—to better understand…