Dear Eric, Thank you very much for your reply and I apologize for this late “thank you”! I am out of town and can not touch the internet during the weekend. I still got several questions here. Would you please help me? 1. The significance of RMSD varies with the numbers of atom pairs, so maybe it makes more sense if I can write out the number of atom pairs at the same time. Is this possible? 2. I think I need the alignment from Match->Align, which better represents the structure alignment. Sorry I kind of got stuck on the output problem, and forgot what I need in the first place. And I am curious about which residues are included in the “core” regions and used for RMSD calculation after turning on the “iterate” option. Can I see this from the Match->Align output? It seems that even if I choose the same cutoff in Match->Align as in iteration, the number of aligned residues is still not the same as the number of atom pairs in RMSD calculation. 3. Also, I am really sorry for not mention this in my first letter -- can I write the transformed PDB file out at the same time? I can only do this with a “.com” file but not a python script. Thank you very much for your help! Have a nice day! Best wishes, Zhiya