SAMSON Blog – Page 315

Focus Without Following: Keeping the Camera Steady in Molecular Animations

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

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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

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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

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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

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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

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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

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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…

Freezing Atoms to Minimize Just Part of a Molecule

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In molecular modeling, it’s not uncommon to need fine-grained control over how parts of a molecule are optimized. Whether you’re modeling a protein undergoing a point mutation, refining a flexible loop while keeping the rest of the structure in place,…

Making Notes Work for You: Mastering ‘Note’ Attributes in SAMSON

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In complex molecular modeling projects, notes are more than just annotations — they often become essential for organizing structural insights, tracking analysis stages, or marking regions of interest. But when your project scales up, managing a growing number of note…

Working on Multiple Molecular Models? This Will Make Life Easier.

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If you’ve ever tried to work on several molecular modeling tasks at once, you’ll know how frustrating it can be to switch between files, copy molecular structures, or compare results side by side. Whether you’re simulating different conformations, comparing docking…