Molecular modelers often explore complex motions of biomolecules to understand conformational changes, such as pocket opening or domain reorientation. These motions are typically investigated through normal mode analysis, but capturing and reusing particular conformations efficiently can be more challenging than expected.
If you’ve ever found yourself scrolling through animations, trying to pause at just the right moment to capture a snapshot of a molecular pose — only to lose it and start over — this post may help. Using the Normal Modes Advanced Extension in SAMSON, you can save interesting conformations, extract structural models, and even export PDB files or full trajectories with precision.
Capture Key Poses Instantly
When you reach a conformation you’d like to keep, just press the S key or use the “store” button to save the molecular pose in the SAMSON document. These saved conformations are accessible nodes in your workspace, allowing fast switching between states for detailed comparison or presentation purposes.
However, if you’re aiming to superpose multiple states or analyze them together, storing conformations isn’t enough. For this, SAMSON lets you convert the selected structure into a structural model. This approach supports direct comparisons between poses, especially useful when exploring how a protein conforms to different ligand bindings.
Generate and Export Trajectories
You can go a step further by storing not just a single conformation, but an entire trajectory of motions. In the “Save frames” tab, define a saving interval to capture frames at specific steps of the normal mode motion. Then choose between:
- Store: to add frames as SAMSON conformations
- Export: to save each frame individually as a PDB file
This flexibility makes it possible to recreate and analyze molecular pathways, or create animations using external visualization tools.
For an even more structured workflow, use the Path button to generate a SAMSON trajectory node. This stores the trajectory in one place and can be played or paused directly from the node list.
Tips and Considerations
When saving frames or exporting states, remember that the saved data reflects your current setting:
- Checked normal modes
- Slider values (amplitudes)
- Scaling factor
- Motion type (linear vs. non-linear, harmonic or not)
- Sampling interval
If you adjust these parameters, you’ll generate a different set of poses — useful for testing hypotheses with variations.
When Is This Useful?
This workflow is especially handy in scenarios where:
- You want to capture a pre-binding conformation of a binding pocket
- You need to compare transitions across multiple normal modes
- You want to export motions for simulation or presentation
Because capturing the right conformation isn’t always straightforward, having the ability to pause, store, export, and replay molecular poses can save hours of work.
To learn more, visit the full documentation for the Normal Modes Advanced extension: 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.