Hello Dr. Shao, The problem you want to avoid is having two or more residues with the same number and chain ID. It is OK if one or the other is the same, but not both. Here are two possible approaches to changing residue numbers and/or chain IDs: (A) If you are familiar with text-editing PDB files, you could just put the two chains in two separate files before opening in Chimera. You don't have to to anything else unless you want a corrected single PDB file for the receptor. Then if you want to make a corrected single PDB file, Chimera can fix numbering and/or chain IDs for you: start the Model Panel (under Favorites) then choose the two models from your two input files on the left, then use "copy/combine" on the right to make them into a single model, and then use "File... Save PDB" in the main menu to save the single file. (B) If you are not comfortable text-editing PDB files yourself, you could instead use one of these PDB-editing web servers to make a corrected single file from your original single file: <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 11, 2011, at 7:09 AM, Qin Shao, Mr. wrote:

Hello I am currently using Chimera 1.5 to analysis docking simulation results from HadDock, because one of my receptor has two chains, it cannot be accepted directly. Through a communication to HadDock, I was advised that I should avoid overlapping numbering between the two chains and use a unique chain ID. Could you tell me whether I can do it on Chimera based on Windows platform, how to do it. Thank you very much. Best regards Dr. Qin Shao