[Chimera-users] MatchMaker-vs-MatchAlign

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 30 10:50:25 PDT 2015

Hello Egor,
The differences are discussed in several places, for example in the MatchMaker manual page:


and details of each are also in their manual pages and our 2006 publication which is linked to the above.  I recommend looking at those for a full understanding, but I will try to summarize as briefly as possible here…

Matchmaker only makes pairwise sequence alignments, and it uses some combination of sequence and secondary structure information.  If the sequences are dissimilar (distantly related proteins) it might be that only small parts of the pairwise alignment are correct, but even so, because of the fit iteration, it can make a good superposition.  If the sequences are fairly similar, however, the Matchmaker pairwise alignments may all be completely correct.  The main purpose of Matchmaker is to superimpose structures, however.  The sequence alignment is just a by-product.

Match->Align then uses only the 3D superposition information: which alpha-carbons are near to which other alpha-carbons. It doesn't pay any attention to the actual sequences.  If the 3D superposition looks good to you, it may be that the Match->Align result will have more correct columns than the Matchmaker result, especially when the sequences are distantly related.  Also, Matchmaker only gives you pairwise, whereas if you have a multiple superposition (>2 structures), Match->Align can give you a multiple alignment (>2 sequences).

Note also you can try using MUSCLE or Clustal Omega web services to realign all the sequences if you want to use only sequence and not structure information in calculating a multiple alignment (from the alignment window menu: Edit… Realign Sequences).

I don't understand your question about RR distance maps.  It makes a distance map, which is a different purpose than Matchmaker (main purpose is superposition) and Match->Align (purpose is to create a sequence alignment from your existing superposition).  In the case of using RR distance maps to compare multiple related structures, it does happen to make a sequence alignment, but currently you can't control any of the sequence alignment parameters, so I wouldn't use it for the purpose of making a sequence alignment.

Also, if you meant you couldn't find the RR distance maps tool at all, if you have Chimera 1.10 or greater it is in the Tools menu under Structure Comparison.

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 Mar 26, 2015, at 1:59 PM, Egor Tchesnokov <tchesnok at ualberta.ca> wrote:

> Hello,
> 1.
> I used MatchMaker to align two structures, worked well and I got an alignment file-1.
> Then I clicked on MatchAlign and got alignment file-2. 
> The alignment-1 is different from alignment-2.
> Could you please let me know what is the differnce between MatchMaker and MatchAlign?
> 2.
> In the same function I can't find RR distance map. Is it applicable to MatchMaker/MatchAlign?
> Thank you
> Egor

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