Efficiently Saving Molecular Trajectories in SAMSON.

For molecular modelers exploring the dynamic motions of biomolecules, capturing and preserving key conformations or trajectories is essential. Whether it’s analyzing intermediate states during binding-site opening or saving entire motion trajectories, SAMSON provides powerful features to store, retrieve, and export these molecular configurations effortlessly. Here’s how you can use its tools efficiently.

Why Save Molecular Trajectories?

During molecular dynamics or normal mode analyses, identifying pivotal conformations that elucidate transitions between states can be crucial. Saving such states allows researchers to revisit, analyze, and build on them without having to repeat calculations. SAMSON’s Normal Modes Advanced module gives you a variety of ways to store, save, or export these configurations, providing flexibility for future work.

Storing Conformations Directly in SAMSON

Found an interesting molecular conformation? You can quickly store it in the document using a shortcut (S). These SAMSON conformations allow for rapid restoration of saved states within your session.

Here’s how it works:

  • Perform your normal mode analysis and manipulate molecular motions using the mode sliders.
  • Once you’ve reached a conformation of interest, press the shortcut (S) to store the structure.
  • Simply double-click the stored conformation in the document panel to restore it instantly whenever needed.

Saving a conformation

Bear in mind, though, that SAMSON conformations do not support superimposing multiple states concurrently. For comparing states, exporting them as structural models might be a better choice.

Exporting Molecular Structures as Models

If you wish to perform analyses that involve superimposing structures or external processing, consider exporting conformations:

  • Select the entire molecule—or just the residues of interest.
  • Use the create button in the module to generate a SAMSON structural model for the conformation.
  • You can also export the current conformation as a PDB file using the export button.

Creating structures

Saving and Exporting Trajectories

Conformations aren’t the only thing you can save—entire trajectories can also be stored or exported for later use. This is particularly useful while studying continuous molecular motions over time.

To save trajectories:

  • Go to the save frames tab in the module.
  • Set the saving interval depending on how many intermediate steps you wish to keep.
  • Click the store button to save the frames as SAMSON conformations.
  • Alternatively, export all frames as PDB files by clicking the export button.

Creating conformations along the trajectory

The Path button allows you to save trajectories as SAMSON trajectory nodes. Double-clicking a trajectory node will play or pause the trajectory using the motion settings you’ve defined.

Creating the trajectory

Final Notes

Whether you’re working with individual conformations or entire trajectories, SAMSON’s tools make it easy to store, retrieve, and analyze your data at any point. Ready to dive deeper into molecular motion exploration? Visit the original documentation for a comprehensive guide.

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

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