Dear Eric,<br><br>Thank you very much for your reply and I apologize for this late ˇ°thank youˇ±! I am out of town and can not touch the internet during the weekend. <br><br>I still got several questions here. Would you please help me?<br>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? <br>2. I think I need the alignment from Match-&gt;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 ˇ°coreˇ± regions and used for RMSD calculation after turning on the ˇ°iterateˇ± option. Can I see this from the Match-&gt;Align output? It seems that even if I choose the same cutoff in Match-&gt;Align as in iteration, the number of aligned residues is still not the same as the number of atom pairs in RMSD calculation. <br>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 ˇ°.comˇ± file but not a python script. <br><br>Thank you very much for your help!<br><br>Have a nice day!<br><br>Best wishes,<br>Zhiya<br><br><!-- footer --><br>