If you’ve ever attempted protein conformation interpolation in SAMSON using the ARAP Interpolator, only to be blocked by an error like “Cannot proceed because the structure does not make one connected component”, you’re not alone. Many molecular modelers encounter this issue when their structures still contain water molecules, ligands, or ions that make the system disconnected. The fix? A simple yet critical preprocessing step — structure cleaning.
Why is structure cleaning needed?
Protein structures downloaded from the PDB often include additional components like ligands, water molecules, and ions. While these can be essential for certain studies, they interfere with structural interpolation because they are not covalently connected to the rest of the structure. For algorithms like As-Rigid-As-Possible (ARAP) interpolation, connectivity is essential to compute a coherent transformation path.
If your input structures contain disconnected fragments, the ARAP algorithm cannot construct a proper graph for interpolation — and you’ll get an error.
How to clean protein structures in SAMSON
Here’s how to prepare your protein structures with a few quick actions in SAMSON:
- Go to Home > Prepare.
- This will remove alternate locations, water molecules, ligands, and ions from your structure.
Still seeing chain fragments you don’t need? You can manually delete them from the Document view — for example, delete the unwanted chain B in the 1MDT structure by selecting it and pressing Del.
When should you do this?
Structure preparation is typically the first step before interpolation. If using two PDB entries as your start and goal conformations (like 1DDT and 1MDT), clean both of them before proceeding.
After cleaning, use the Conformation feature to name and store your cleaned versions (e.g., “1DDT A” and “1MDT A”) as interpolation endpoints. From there, the rest of the ARAP Path Interpolation setup can move forward smoothly.
How to avoid errors and save time
By making protein structure preparation a regular part of your workflow, you eliminate this common barrier and save valuable time. It ensures that your ARAP interpolation — or any simulation depending on clean, connected structures — runs without interruptions.
To learn more about structure preparation in SAMSON, watch this step covered in the full tutorial on ARAP interpolation: documentation.samson-connect.net/tutorials/arap/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.