Hi everyone,

I am currently working on merging protein structures obtained from multiple X-ray diffraction datasets. After refinement, I noticed that there are some structural differences between the two atomic models. I would like to compare these structures using RMSD.

In particular, since my protein is mainly composed of α-helices, I would like to generate a “helix-wise RMSD” (per-helix RMSD) to emphasize which helices contribute the most to the structural differences.

Could anyone recommend suitable software or tools (GUI-based or scriptable) that can help me calculate both overall RMSD and helix-specific RMSD? Any suggestions or example workflows would be greatly appreciated!

Thanks in advance.