[Chimera-users] residue order for match/rmsd

Klaus Kopec klaus.kopec at tuebingen.mpg.de
Tue May 19 09:52:17 PDT 2009

Hello again,

the way you explained it works like a charm, thanks for that!

I just assumed the match command to keep the sorting of the command 
line, as sorting the residues by number did not make any sense to me ;)

Thanks again,

Elaine Meng wrote:
> 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!)
> <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>
> I hope this helps,
> Elaine
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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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