[Chimera-users] residue order for match/rmsd

Klaus Kopec klaus.kopec at tuebingen.mpg.de
Tue May 19 08:09:34 PDT 2009

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 at CA 
#1:3,2,1 at 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!

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.

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