In molecular modeling and dynamics simulations, creating multiple replicas of a protein system is often necessary, especially when working with coarse-grained models to simulate complex systems. However, for many researchers, this process might feel daunting, as it involves more than just duplication. Properly setting up replicas means ensuring structural integrity, unique chain IDs, and residue numbering.
In this guide, we’ll walk you through a detailed process for creating replicas manually within SAMSON using the example of Ubiquitin protein (1UBQ), highlighting best practices and common pitfalls.
A Step-by-Step Approach
Step 1: Visualize the Full Atomic Structure
Begin by ensuring that all atoms in your structural model are fully visible. This will make it easier to copy chains without missing elements. You can toggle the structural model’s visibility by checking and unchecking the checkbox of the model, as shown in the image below:
This will result in a fully visible atomic structure:
Step 2: Select and Copy Chains
Now, select the chain(s) you would like to replicate. Once selected, use the shortcut Ctrl/Cmd + C (to copy) and then Ctrl/Cmd + V (to paste). SAMSON will create a new copy of the chain directly in its original position. Here is an example of a copied chain:
Step 3: Move the Replica
With the newly copied chain still selected, switch to one of SAMSON’s move editors, like the Global Move Editor (shortcut K). Then, adjust the positioning of the duplicated chain to avoid overlaps:
If needed, you can enable translational and rotational snapping to achieve precise placements.
Step 4: Repeat as Necessary
Repeat Steps 2 and 3 until you have created the desired number of replicas. SAMSON also supports copying and moving multiple chains simultaneously, reducing repetitive actions:
Renumbering Chains and Residues
After creating the replicas, ensure that chain and residue IDs are unique to avoid conflicts during modeling or simulation processes. Here’s how:
- Renumber Residue IDs: Right-click on the structural model and select Structural model > Renumber residues and structural groups. Set the starting number (default is 1) in the dialog and click OK.
- Renumber Chain IDs: Similarly, select Structural model > Renumber chain IDs. Set the starting chain ID to 0 and confirm. This ensures all chains have unique IDs.
- Rename Chains: You can rename chains directly in the document view (shortcut F2) or by using SAMSON’s Inspector tool.
Once this process is complete, your system will be ready for coarse-graining or other advanced simulations in SAMSON. Remember to save your work to preserve your progress.
Wrap-Up
With this step-by-step guide, creating replicas for protein systems in SAMSON becomes a straightforward and manageable process. It helps researchers save time while ensuring consistent modeling practices. To learn more, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at SAMSON Connect.