[Chimera-users] Selection of residues and superposition

Alessandra Gastaldello Alessandra.Gastaldello at sib.swiss
Fri Jun 24 06:07:44 PDT 2016

Il 2016-06-23 19:37 Elaine Meng ha scritto:
> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> For more examples, see the “Matching” section in the hydrolases
> image tutorial:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html>
> (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.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
> Summary of the different ways of superimposing structures in Chimera
> and when you might want to use one or the other:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> I hope this helps,
> Elaine
> ----------
> 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!

Thank you so much Elaine! Very helpfull explanation about how to use 
Despite that, I have a problem with some match and selection.
For some protein when I type for example:
match #0:346 at n,ca,o,c #1:23 at n,ca,o,c
to match those atoms in position 346 and 23, chimera tells me that the 
number of atoms is not the same.
How this is possible?

Thank again.

Alessandra Gastaldello
SIB | Swiss Institute of Bioinformatics
CMU - 1, rue Michel Servet - 1211 Geneva 4
t: +41 22 379 50 50 - f: ...
Alessandra.Gastaldello at sib.swiss - http://www.sib.swiss

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