[Chimera-users] Selection of residues and superposition

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 23 10:37:27 PDT 2016

Hi Allessandra,
(A) Instead of selecting, you can use the “match” command and directly specify the residues to match.  It will be a pairwise match, but if you choose one as the reference structure and match the others to it, you will end up with all of them superimposed.  For example, match structure 1 to structure 3, and then match structure 2 to structure 3.  The main difficulty with match is that you have to be careful to give exactly the same total number of atoms for each of the two structures.  It can also be a lot of typing to enter many residue numbers, but you can give ranges.  Example:

match #0:25-35.A,68.A,123.A at n,ca,c,o  #1:28-38.A,80.A,166.A at n,ca,c,o

…. means superimpose model 0 residues 25-35,68,123 of chain A backbone atoms N,CA,C,O onto model 1 residues 28-38,80,166 of chain A backbone atoms N,CA,C,O.  Many variations are possible, the chain IDs in the two structures could be different, and you could use different atoms, maybe only CA.  You can see which structures are which model number in the Model Panel (in menu under Favorites).

“match” command help:

For more examples, see the “Matching” section in the hydrolases image tutorial:

(B) Alternatively, if it is something like whole domains or other long residue ranges, it may be easier to still use MatchMaker with the option "Further restrict matching to current selection” (after selecting those parts).  There is a similar capability in the “matchmaker” command but then instead of selecting you would again need to type in those ranges.

Summary of the different ways of superimposing structures in Chimera and when you might want to use one or the other:

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 Jun 23, 2016, at 9:15 AM, Alessandra Gastaldello <Alessandra.Gastaldello at sib.swiss> wrote:
> Hi,
> I am trying to use Chimera to do superposition of multiple 3D structures.
> What I would really like to do is:
> 1. to select some residues for each of the structure
> and then
> 2. to superimpose the structures telling to chimera that the residues I selected have necessarily to be superimposed.
> To align "only" the protein sequences in a similar way for example I use COBALT that allows to specify the position of residues that have to be aligned necessarily together.
> Can I do this in chimera with 3D structures?
> thank so much for any help!

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