A common challenge in molecular modeling is not just generating motions, but storing them in a meaningful and shareable way. Whether you’re communicating your results to colleagues, preparing figures for publication, or organizing data for further analysis, saving conformational changes along a trajectory can be tedious—especially if the tools are clunky or the process is manual.
That’s where the Normal Modes Advanced Extension in SAMSON comes in. This module provides a streamlined way to save, browse, and export molecular trajectories generated from nonlinear normal mode analysis using the fast and reliable NOLB algorithm. Let’s take a closer look at how to turn simulations into shareable insights.
Save what matters: conformations and trajectories
Once you’ve generated molecular motions via the mode sliders, you’ll often want to preserve a specific conformation. With SAMSON, this couldn’t be simpler. You can press S or click the store button to save a conformation in your document. These conformations are immediately accessible and browsable within the interface.
Need to compare two or more states of your molecular structure? Simply convert conformations into structural models using the create button in the NMAL app. This adds flexibility, particularly when comparing intermediate steps of a motion. The current structure can also be exported as a standard PDB file—ideal for sharing or use in other tools.
Export a full trajectory
Sometimes you’ll want to save not just a single conformation, but the entire trajectory across its motion path. To do this, navigate to the save frames tab inside the module. Here you can:
- Set the saving interval between conformations
- Click store to save as a set of conformations within SAMSON
- Click export to save the trajectory as a series of PDB files
Each conformation node is interactive—double-clicking will instantly display the corresponding structure. If your workspace becomes crowded, clean-up is easy with the remove button.
Optional: Package as a trajectory node
If you prefer working with animations, the entire motion can be packed into a single trajectory node by using the Path button. This allows easy review: double-click to play, pause, or scrub the motion. You can manage the visibility and playback without cluttering your project with multiple structure copies.
Everything under control
All saved or exported data reflects your current settings—from the selected normal modes and scaling factor to the motion type and saving interval—giving you precise control over what’s preserved.
Whether you’re visualizing the opening of a protein’s binding site or exploring flexibility for drug docking, these export features make it easy to document your work and share it with others.
To learn more about these features and how to use them, visit the full tutorial 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 download SAMSON at https://www.samson-connect.net.