Modeling Protein Replicas Faster with SAMSON’s Martinize2 Extension

Creating coarse-grained models of large molecular systems often requires not one, but many replicas of the same protein. This is a common setup when studying aggregation, protein crowding, or behavior in complex environments. But preparing these systems—ensuring residue IDs don’t clash and chain names remain unique—can be a tedious and error-prone manual process.

If this sounds familiar, good news: the Martinize2 Extension in SAMSON makes this significantly easier. Here’s how you can streamline the process of preparing multiple replicas for coarse-graining with MARTINI, all inside the SAMSON interface.

Step 1: Make Your Protein Visible

Begin by loading your protein structure into SAMSON. To ensure you can duplicate chains effectively, make all atoms visible by toggling the structural model visibility—uncheck and recheck its box in the document view. This ensures clear selection and placement of replicas.

Visible structural model

Step 2: Create Replicas with Copy-Paste

  1. Select the chain or chains you want to replicate.
  2. Press Ctrl/Cmd + C to copy, then Ctrl/Cmd + V to paste. The new chain will appear in the same location.
  3. Use move editors like the Global Move Editor (K) to reposition the replica.

Repeat this process to create as many copies as you need. You can also move multiple chains at once to speed things up.

Create multiple replicas

Step 3: Renumber Residues and Chain IDs

This is a crucial step. Without unique residue and chain IDs, the topology generation may fail or produce incorrect structures.

  1. Right-click the structural model and choose Structural model > Renumber residues and structural groups. Set the starting number (default is 1) and click OK.
  2. Then, in the same menu, select Structural model > Renumber chain IDs and confirm.
  3. To rename chains, either press F2 on the chain in the document or use the Inspector.

Renumber residue IDs

This ensures all replicas will be treated as distinct during topology generation.

Ready for Coarse-Graining

Once your replicas are in place, uniquely numbered, and cleanly separated, you can proceed to create CG models by following the regular Martinize2 workflow in SAMSON. Select your system, set options, and click Create coarse-grained models.

Learn more in the full documentation here: https://documentation.samson-connect.net/tutorials/martinize2/martinize2/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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