When exploring molecular motions, one common challenge for modelers is how to effectively capture and reuse intermediate or final conformations. Whether you’re inspecting how a ligand access channel opens, or evaluating different configurations of a flexible loop, you often find “interesting” states that you’d like to keep — or come back to later.
This blog post covers how to save, revisit, and export such conformations using the Normal Modes Advanced Extension in SAMSON. These features can help you document your workflow, prepare figures, or generate input files for further simulation.
🧬 The basic saving feature: storing conformations
Once you’ve found a conformation you’d like to keep during your exploration of normal modes, the quickest way to store it is by using the shortcut S or clicking the appropriate button in the module. This saves the current state of the structure in the document as a SAMSON conformation.
These conformations are convenient to use. You can activate a saved state just by double-clicking on it. This makes them especially useful when you’re comparing different configurations of a loop, pocket, or domain during a session.
🧩 Beyond saving: creating structures for comparison
If you want to superpose multiple states — for example, pre- and post-opening of a binding site — you’ll need more than just stored conformations. This is where the structural model feature comes in.
To create one, select the desired atoms or the full structure and press Create in the NMAL app. This generates an identifiable structure in the document, which can then be compared, visualized, or exported independently of the rest of the trajectory.
💾 Exporting to PDB
Need the coordinate files? You can export the current structure state directly as a PDB. This is helpful for post-processing, documentation, or if you need the conformation outside of SAMSON (e.g., for docking experiments or energy minimization).
The export function ensures you maintain compatibility with a wide range of external tools — from visualization to molecular dynamics packages.
📽️ Saving entire trajectories
Sometimes, it’s not just about a single snapshot. The entire transition from one conformation to another might be of interest — and SAMSON enables you to store whole trajectories. Simply open the Save Frames tab and specify your saving interval.
You then have two saving options:
- Store the trajectory as a series of SAMSON conformations
- Export each frame as a PDB file
Double-clicking on any of the stored conformations brings it into view; you can also remove them if needed to keep things organized.
➡️ Store the path itself
Lastly, the Path button allows you to encapsulate a whole transition into a dedicated SAMSON trajectory node. This is a convenient way to playback the full motion and share it with a colleague or use it in a presentation.
Putting it all together
Knowing how to save individual conformations and entire motion paths in SAMSON can drastically improve your productivity. Whether you’re doing structural comparisons, preparing data for downstream analysis, or simply want to keep a record of an exploratory session — these tools are here to help.
To learn more, visit the official documentation at https://documentation.samson-connect.net/tutorials/nma/calculating-non-linear-normal-modes/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net