Studying protein conformational changes often means diving into large simulation datasets and sorting through movement trajectories, energy variations, and transition intermediates. For many molecular modelers, a common pain point arises once a path between two protein conformations has been computed: how can I extract meaningful, reusable data from this path?
Whether you’re preparing figures for a publication, comparing alternative transition routes, or feeding information into another simulation pipeline, exporting clean, relevant data is key. SAMSON’s Protein Path Finder app includes a set of export tools designed to make this straightforward.
What can be exported?
Once a conformational path has been calculated between a start and goal structure, SAMSON’s Results tab opens up several possibilities:
- Copy path summary: Get all energy metrics associated with each path directly to your clipboard.
- Export entire paths as trajectories: Add these to your SAMSON document for visualization or further processing.
- Export conformations along the path: Select your desired resolution (e.g., every Nth frame) and insert these as snapshots.
This means you can easily compile data for your analysis—including Minimum and Maximum energy, energy differences (barriers and saddles), time taken per path, and the number of conformations associated with each transition route.
Step-by-step: Exporting from the Path Finder
- Select paths you’re interested in from the Results table.
- Right-click to bring up export options:
- “Copy table content”: copies the full path information
- “Copy path energy”: extracts the energy per state
- Click Export paths to send the calculated path as a new trajectory into your document structure.
- Want structure files? Use the export conformations feature to save PDBs of steps along the transition (customizable to your interval).
Why it matters
Without proper export tools, valuable computed paths might be stuck in a sandbox, making it hard to share findings or continue analyses in other tools. With structured export capabilities, SAMSON bridges this gap and supports the full molecule modeling workflow: from transition prediction to analysis and sharing.
Additionally, if you are interested only in selected atoms (say, backbone CA positions or specific loop regions), the Export Along Paths SAMSON Extension can help generate tailored trajectory exports. You can choose which atoms to track across the computed path, potentially feeding this output into comparative studies or external force field refinements.
Final thoughts
Knowing how to extract and share your computed results is part of working efficiently in molecular modeling. The Protein Path Finder ensures you’re not limited to viewing transition paths inside the app—you can carry your computed knowledge to other tools, share it with collaborators, or archive it for future reference.
To dive deeper into the capabilities of the Protein Path Finder app, check out the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.