When working on molecular modeling projects, especially those involving proteins or nucleic acids, one frequent task is to simulate structural flexibility and then extract useful conformations. After exploring different conformations through normal mode analysis (NMA), many researchers hit a familiar bottleneck: How do you save the most relevant states clearly and reliably for further simulations, sharing, or publications?
In this post, we’ll explore how to save and export conformations—or even entire motion trajectories—using the Normal Modes Advanced Extension in SAMSON. Whether you want to quick-save a snapshot or build a full trajectory dataset, SAMSON gives you multiple tools to capture your results from nonlinear NMA simulations.
Quick Saving Conformations
When you find an interesting conformation during a normal mode simulation—perhaps as two protein domains move apart—you can store that conformation directly into the current SAMSON document. Pressing S saves the current atomic positions, allowing you to restore them later within the same modeling session.
This method is fast and convenient, but keep in mind it’s best suited for internal reference. If you need to compare multiple states or use them outside of SAMSON, the next step provides more flexibility.
Creating Structural Models and Exporting to PDB
To save your current structure as a static model, select all or part of the molecule and click the Create button in the NMAL extension. This action creates a structural model that can be managed independently.
If you need the structure for use in other programs (e.g., GROMACS, ChimeraX), SAMSON lets you export the selected conformation as a PDB file directly. Just hit the Export button and choose your destination.
Saving Full Trajectories
If you don’t want to limit yourself to single frames and are working with animations of structural motion, you can save the entire trajectory.
In the Save Frames section, you can:
- Set a saving interval (e.g., save every 5th frame).
- Store all intermediate conformations in the SAMSON document.
- Export the trajectory as multiple PDB files.
This approach is particularly useful if you want to analyze the full dynamics path, feed it into an external simulation workflow, or just visualize the progression in another tool. You can also create a SAMSON trajectory node using the Path button, allowing for playback within the platform:
Final Thoughts
The ability to selectively store, group, and export molecular conformations vastly improves production workflows in molecular modeling. Whether you’re preparing figures for publication, designing experiments, or sharing with collaborators, SAMSON’s flexible export features allow you to keep your structure data organized and accessible.
Learn more about nonlinear normal mode analysis and exporting motion data in SAMSON by visiting the full documentation page: SAMSON NMA documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.