One of the challenges structural biologists often face is not only computing and visualizing protein motions, but also saving them in a way that is easy to analyze, compare, or share with collaborators. Whether you’re studying conformational transitions or designing animations for presentations, exporting a trajectory as a series of PDB files can be extremely helpful.
The Normal Modes Advanced extension in SAMSON offers a streamlined approach to saving trajectories of molecular motions governed by nonlinear normal modes. This blog post walks you through how to save a molecular motion trajectory as a series of PDB files using the plugin’s Save Frames tab.
Why Save a Trajectory?
When working on molecular modeling projects, animations of structural transitions can provide clearer insights into potential binding events or functional changes. Exporting these as PDB files allows further analysis using third-party software (e.g., PyMOL, VMD) or supports generating figures and movies.
Step-by-step: Exporting Trajectories in PDB Format
- Compute Normal Modes: Begin by loading your structure (e.g., 1VPK) and computing its nonlinear normal modes using the Normal Modes Advanced extension. Set the number of modes, interaction cutoff, and potential type.
- Set Up the Motion: Use the sliders to combine various modes. Observe the structure responding to these changes in real time. You can scale the amplitude of the motion and switch between linear or nonlinear transformations.
- Open the “Save Frames” Tab: In this tab, define the saving interval—this determines how frequently frames are saved along the trajectory.
- Export as PDB: Click the export button to save the entire trajectory as a set of PDB files. Each frame will represent a conformation along the selected path with the applied modes and parameters.
Additional Features
- You can also store the trajectory within SAMSON as a trajectory node, available for playback by double-clicking.
- The trajectory export respects all motion parameters: checked modes, values of sliders, motion types (harmonic or not), and scaling factors.
- If needed, you can create SAMSON conformations or structural models to visualize intermediate states quickly.
Tips
- Make sure only the modes you want are checked and adjusted before exporting—unchecked sliders won’t affect the saved trajectory.
- Exported PDB files are useful for aligning conformations or generating movies using other software packages.
By exporting trajectories in this way, you can document conformational pathways, prepare data for presentations, or share specific structural motions with collaborators for interpretation.
To learn more about working with nonlinear normal modes and trajectory export in SAMSON, visit the full documentation page: 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.