One of the challenges faced by molecular modelers is saving and exporting molecular conformations and trajectories efficiently while maintaining flexibility for further analysis. If you’re exploring molecular motions in SAMSON using the Normal Modes Advanced (NMA) extension, you’ll be glad to know there are powerful tools available to help you save and export resulting structures and trajectories for downstream applications or publications. Let’s dive into the process and features you can leverage.
Storing Interesting Conformations
When you identify an interesting conformation, you can quickly store it in SAMSON’s structure document by simply using the shortcut S. Saving conformations in this way allows for rapid restoration of desired structural states whenever needed:
However, SAMSON conformations cannot be superposed for comparative visualization. This is where creating structural models comes in handy.
Creating Structural Models and PDB Export
To generate a SAMSON structural model, you can select the entire structure—or specific regions of interest—and click the Create button in the NMA module. This feature helps you focus on specific structural changes and refine your analysis. Moreover, the current structure can be exported directly as a PDB file using the Export button:
Saving Trajectories
Exploring dynamic biomolecular motions often involves generating trajectories. SAMSON makes it easy to save an entire trajectory. Here’s how:
- Set the saving interval in the Save Frames tab of the NMA module.
- Store the trajectory as a set of conformations using the Store button, or export the trajectory as PDB files with the Export button.
Conformations along the trajectory appear as nodes, allowing you to double-click to display individual states instantly. Removing unwanted conformation nodes is just as straightforward with the Remove button:
Advanced: Storing Complete Trajectories as Nodes
Another advanced feature allows storing the entire trajectory as a single SAMSON trajectory node by clicking the Path button. This node supports visualization of dynamic trajectories within the SAMSON environment, giving you more flexibility to analyze molecular motions:
Playing and pausing the dynamic trajectory is as simple as double-clicking on the trajectory node.
Customizing Saved Trajectories
The outputs—conformations and trajectory files—are influenced by the settings in the Calculations tab at the time of saving. These include:
- Checked modes and their slider values.
- The scaling factor for motion amplitudes.
- The type of motion (e.g., harmonic or non-harmonic).
- The saving interval.
This level of control gives you the ability to tailor outputs to match your specific analysis needs.
Conclusion
With SAMSON’s NMA module, you can seamlessly manage molecular trajectories and structural conformations, from saving snapshots to exporting PDB files or entire dynamic paths. These tools make it much easier to maintain an organized workflow and communicate your structural findings with high-quality data formats. To learn more about additional features, visit the original documentation page at this link.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.