I am trying to linearize certain residues of the protein. So, to minimize the disturbance while linearizing the residues, I have created the grids with a distance of 5 Armstrong around the protein to identify the best direction to unfold. Initially, I created boundaries around the protein. Each grid consists of sets of residues that fall inside that grid.
Reference Question: How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
The problem I'm facing:
- I am unsure how to effectively use the grid to determine the smoothest unfolding direction.
- As an example I took the PDB ID: 4fdi and the sequence size is 522. When unfolding certain segments (e.g., residues 342–361), the entire chain shifts out of the container, as seen in Image 1. However, when unfolding a more centrally located segment (e.g., 241–260), the code works correctly without displacing the rest of the chain. In another case (e.g., residues 91–110), 90% of the chain moves out of the compartment, while the remaining 10% collapses into another chain. Instead, this 10% should move out of the compartment, as shown in Image 2., as shown in Image 2.
I truly appreciate any help from the experts
You can find the complete code on my GitHub account: https://github.com/aspergillus/Targeted-MD-Stimulation/blob/main/unfolding_protein_script.py
Image 1: Unfold on residues 342–361
Image 2: Unfold on residues 91–110
