[Chimera-users] about the command: match

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 5 11:11:48 PDT 2013

Dear Xiaodong Han,
I can only repeat what the  message says:  apparently your "site1" and "site2" do not specify the same numbers of atoms.  You can check, for example, by using command:
select site1
… and then seeing how many atoms are selected, then
select site2
… and then seeing how many atoms are selected.

Even though these two words "site1" and "site2", which I assume are aliases that you made, may refer to exactly the same residue numbers, sometimes a structure will have missing atoms, or atoms with multiple "alternate location" copies, or maybe they are different proteins with different residues that contain different numbers of atoms.  For example, an arginine has many more atoms than a glycine. Or, maybe (accidentally) your specifier includes water in one structure and not the other. You will have to make specifiers that give equal numbers of atoms as each other because "match" will not figure out the pairing for you.  


If you want something to figure out the pairing for you, and you are matching two biopolymers (i.e. two proteins or two nucleic acid chains), you may want to use the "matchmaker" command (or tool) instead.  Here is a discussion of the different methods for superposition.

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

On Sep 5, 2013, at 7:50 AM, 韩晓东 <hxdon at 126.com> wrote:

> Dear sir,
> it is no doubt the UCSF chimera is a very excellent software. However, when i use the command: match iterate 2.0 site2 site1, a problem appeared as follows: unequal numbers of atoms chosen for evaluation. would you kindly share me the skill to deal with this problem. thank you very much for your time.
> sincerely yours,
> xiaodong han.

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