How to change the rotamer state of side chains (April 23, 2025)

Estimated read time: 2 minutes.

Question: I want to rotate some residue side chains in the binding site before docking. How can I change the rotamer state?

Answer: Protein side chains can adopt different spatial orientations, or rotamers. For docking, changing the rotamer state can help eliminate steric clashes between residues or adjust the size of the ligand-binding site to achieve your desired results. The 3D & Analyze Page in Orion makes this process easy by allowing you to quickly visualize different rotamer states and select the optimal one in just a few simple steps.

Here’s how:

_images/Orion_Tip_Rotamer_01.png
_images/Orion_Tip_Rotamer_02.png
_images/Orion_Tip_Rotamer_03.png

To learn more, visit the 3D & Analyze page documentation to learn more about 3D editing in Orion.