[Chimera-users] residue order for match/rmsd

Elaine Meng meng at cgl.ucsf.edu
Tue May 19 09:19:05 PDT 2009

Hi Klaus,
Thanks for the compliments!

In the production release 1.3 and earlier versions of Chimera, commas  
do not imply ordering. To guarantee the order you would need to use  
(continuing your example):

match #0:1 at ca:2 at ca:3 at ca #1:3 at ca:2 at ca:1 at ca

However, if you get a recent daily build, it will behave the way you  
expected:  commas will imply ordering.  You might have been looking  
at a manual page for this newer version.  To use the manual pages  
that go with your download, use the Chimera "Help" menu.

In the list of what changed since release 1.3, this ordering issue is  
under "Command Changes" (not that I would expect you to have found  
this yourself... just thought you might be interested!)

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 19, 2009, at 7:27 AM, Klaus Kopec wrote:

> 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!
> 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.

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