When modeling the flexibility of biomolecules, it’s common to analyze and generate alternative conformations that represent plausible intermediate or functional states. However, there’s often a challenge that arises: once you’ve arrived at an interesting conformation or motion through computational tools, how can you easily save, export, and share it?
In molecular modeling workflows, efficiently handling multiple conformations and trajectories is crucial — especially when working with collaborators or preparing figures for publications. This blog post focuses on a subset of SAMSON’s Normal Modes Advanced extension functionalities: how to save, export and manage generated conformations and motion trajectories.
Storing Conformations Inside the Project
The fastest way to save a structure that you’ve manipulated or reached using normal mode exploration is to store it as a SAMSON conformation. A quick press of the S key lets you capture the current state of your structure. These conformations are stored in your document, and can be restored later with a double-click.
Keep in mind, however, that SAMSON conformations are specific to the document—they do not allow for superposition of different states unless a structural model is created (more below).
Creating Structural Models
If you want to compare several molecular states (e.g., open/closed binding pockets, different positions along a normal mode), you can convert the current structure into a structural model. To do this, simply select the region of interest and click the create button in the NMAL (Normal Modes Advanced) app.
This function allows you to keep multiple conformations side-by-side, making structural comparisons much easier.
Exporting as PDB Files
If you need to move your work outside SAMSON (e.g., for further analysis in PyMOL, VMD, or refinement software), just press the export button to save your current conformation or structure as a standard PDB file. This ensures maximum compatibility with a wide range of molecular visualization and modeling tools.
Storing Trajectories
The Normal Modes Advanced extension also lets you save not just single conformations, but entire motion trajectories as the structure explores its deformation space.
In the save frames tab, you can choose your desired saving interval and then either store conformations as part of the SAMSON document or export them as a series of PDBs.
You can also click the Path button to group the entire trajectory into a dedicated trajectory node, which you can play or pause.
Whether you’re reporting a structure opening, closing mechanism, or movement derived from a set of normal modes, this workflow allows you to preserve and communicate your findings clearly.
Conclusion
Being able to store and export conformations and motion trajectories is a key part of integrative modeling workflows. The flexibility provided by SAMSON — from in-app conformations, structural model creation, to PDB export — makes it easier to retain, compare, and share meaningful structural insights.
To see a visual walkthrough and explore more options, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.