Molecular modelers often face the challenging task of creating multiple replicas of the same structure for simulation purposes. Replicas are crucial when studying complex systems, yet their creation can be time-consuming and prone to errors like overlapping chains or incorrect residue numbering. Luckily, SAMSON provides an efficient, user-friendly workflow for creating and managing replicas manually, ensuring accurate preparation for simulations.
In this blog post, we’ll guide you through the process of creating replicas manually in SAMSON, covering chain duplication, positioning, and ensuring uniqueness in chain IDs and residue numbers. This tutorial empowers you to save time and avoid common pitfalls.
Beginning with Atomic Structure Visibility
Before creating replicas, make sure all atoms in the structure are visible. This ensures a clear view while copying and placing the replicas. Toggle the visibility of the structural model by unchecking and checking its visibility in the document view:
This will result in a fully visible atomic structure:
Step 1: Copy Chains to Create Initial Replicas
Select the chain(s) of interest from the structural model in the document view:
Use the Ctrl/Cmd+C and Ctrl/Cmd+V shortcuts to copy and paste the chain. A new copy will appear in the same position.
Step 2: Position Each Replica
After copying a chain, use the Global Move Editor (K shortcut) to move the new replica to a desired position. Adjust snapping options in the viewport to control translational and rotational movements:
Repeat the copy-and-move process until the desired number of replicas is created. You can even copy and move multiple chains simultaneously:
Step 3: Ensure Unique Residue and Chain IDs
To prevent issues during topology generation, each chain and residue in the system must have unique IDs.
- Renumber Residue IDs: Right-click the structural model, select Structural model > Renumber residues and structural groups, and set the starting value to
1. - Renumber Chain IDs: Right-click the structural model, go to Structural model > Renumber chain IDs, and keep the starting value as
0. - Rename Chains: Rename chains individually in the document via
F2or the Inspector:
Save Your Progress
After creating and renumbering replicas, save your system into a file to preserve your work and ensure no repetitions in future steps.
What’s Next?
Once your replicas are ready, you can continue to coarse-grain them with the Martinize2 Extension in SAMSON. Follow the step-by-step process detailed in the documentation here.
Learn more at the original documentation page: SAMSON Martinize2 Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON for free at SAMSON Connect.