Capturing molecular flexibility is an essential part of modern structural biology and computational modeling. Whether you’re exploring ligand accessibility, visualizing allosteric motions, or preparing morphing animations between conformations, there often comes a time when you reach an interesting molecular state — and you need to save it. But how exactly can you store or export that conformation, especially when it’s not just about coordinates but also about the context in which they were generated? That’s where the Normal Modes Advanced extension in SAMSON can help.
This article explores how to practically save and export conformations and trajectories from your simulations using SAMSON’s normal mode analysis tools. If you often ask yourself: “How do I keep this conformation for later? How do I compare multiple states?” — read on. We’ll walk through the relevant features so you don’t lose your valuable trajectory data.
Saving a Conformation
When you have moved along a normal mode or a combination of modes to reach a molecular conformation of interest, SAMSON allows you to quickly store this specific state by pressing S or by using a button within the module interface. This adds the conformation to your document so you can easily restore it later.
This is useful for quickly bookmarking interesting poses directly within your modeling session. However, note that this method is optimal for individual snapshots — if your objective is to compare multiple states side-by-side or across time, you’ll want to go a step further.
Creating Structural Models
To capture multiple conformations in a way that allows superposition and more advanced comparison, you can create a structural model. Simply select the entire molecule or the region of interest and click the create button within the NMAL app. This saves the structure as an independent model in your document.
You can also export your conformation as a standard .pdb file using the export button, making it suitable for analysis in other tools or environments.
Exporting a Trajectory
If you’ve explored a dynamic transition across multiple normal modes, it can be helpful to save the entire trajectory. Go to the save frames tab, where you can define a saving interval (i.e., how often a snapshot is taken along a trajectory). You have two options:
- Store snapshots inside SAMSON as conformations.
- Export the snapshots as
.pdbfiles for use in other programs.
Once you’ve stored these conformations, you can double-click on any of them in the document to view them instantly. You can also clean up the workspace using the remove button to delete unwanted or outdated conformations.
Storing the Full Trajectory
If you’re working with more continuous motions (as in morphing between two states), the Path button lets you store your entire trajectory as a trajectory node in SAMSON. By double-clicking on this node, you can play or pause the motion to review how the structure evolves.
Keep in mind: everything you save is based on your current settings — including which modes are active via checkboxes, the values of the mode sliders, the scaling factor, and whether harmonic motion is enabled. To reproduce a trajectory, these need to be consistent.
Tips for Molecular Modelers
- If you’re preparing a figure, isolate and store key conformations using the create and export buttons.
- Want to visually compare flexibility between states? Save multiple conformations and superpose them as different structural models.
- For longer motions, trajectory nodes provide a clear representation — even enabling play/pause control for animations.
Careful saving and exporting of motion data helps streamline communication with collaborators, presentation preparation, or further analysis in external tools. SAMSON’s integrated approach makes this convenient within the same modeling session.
Learn more in the original SAMSON documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.