Hi everybody, at first I would like to thank you for Chimera, it's the best structure viewer I am aware of! Now to my question: I would like to match residues in two structures, but not in the numerical order. My expectation was that if I run "match #0:1,2,3@CA #1:3,2,1@CA" I would end up with least squares fitted coordinate pairs (#0:1, #1:3), (#0:2, #1:2) and (#0:3, #1:1). What I get, however, is a least-squares fit of pairs (#0:1, #1:1), (#0:2, #1:2) and (#0:1, #1:3). Is it possible to use the order of coordinate pairs given in the command line (e.g. pair first specified coordinate of protein 1 with first specified coordinate of protein 2, second with second, etc.) instead of the numerical order of the residue numbers? I would be really glad if someone could help me out on this! Klaus PS: I use Chimera 1.3.2577 under a 64-Bit Kubuntu. I also tried some older (1.2.something) version which gave the same results.