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, Klaus 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@ca:2@ca:3@ca #1:3@ca:2@ca:1@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@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@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.