Saving Molecular Flexibility: How to Export Conformations and Trajectories in SAMSON

One of the challenges many molecular modelers face when analyzing the flexibility and dynamics of biomolecules is keeping track of interesting conformations or motion trajectories. Whether you’re preparing a figure for publication, comparing several states of your molecule, or simply organizing your simulations, exporting structural conformations and trajectories efficiently can make a big difference.

If you’re using the Normal Modes Advanced extension in SAMSON, you have multiple ways to capture and store the results of your nonlinear normal mode analyses. Here’s a breakdown of the different options available, so you can find the most suitable method for your workflow.

Storing Interesting Conformations

Once you’ve adjusted the mode sliders to a specific structural configuration that opens a binding site or matches a target conformation, you may want to keep that state for future use. You can:

  • Store the conformation in the document using the S keyboard shortcut.
  • This lets you quickly restore that state later, similar to bookmarks in your structure exploration.

Saving a conformation

Creating Structural Models

While storing conformations in SAMSON is helpful, it doesn’t allow direct visual comparison between multiple states. To do that, you can:

  • Create a structural model from the selected part of the molecule or the whole structure.
  • This allows for superposing various states, useful for comparing closed vs open conformations, or pre- and post-binding states.
  • You can also export this structure as a PDB file using the “export” button.

Creating structures

Exporting Full Trajectories

If your goal is to capture the full dynamic behavior (not just one snapshot), SAMSON offers two main ways to store a trajectory:

  • Go to the save frames tab and define a saving interval (i.e. how many frames to store).
  • Store: Saves internal SAMSON conformations representing frames along the motion.
  • Export: Outputs a series of PDB files representing each frame for downstream processing in third-party tools or visualization software.

Creating conformations along the trajectory

Playing and Managing Trajectories

Once stored, trajectories can be managed and replayed from within SAMSON:

  • Use the Path button to consolidate frames into a SAMSON trajectory node.
  • Double-clicking the trajectory node allows you to play or pause motion sequences.

Creating the trajectory

It’s worth noting that the saved trajectory or conformation reflects your current settings in the calculations tab — including which modes are checked, their slider values, the scaling factor, the motion type (harmonic or not), and the frame saving interval. So make sure your setup reflects the insight you want to export.

Exporting flexible molecular structures shouldn’t be a chore. With these export tools in the Normal Modes Advanced module, you can retain and share your findings more efficiently — whether you’re preparing figures, running simulations, or collaborating with colleagues.

To learn more about how to use the Normal Modes Advanced module for trajectory and conformation export, visit the official documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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