[Chimera-users] MatchMaker-vs-MatchAlign

Egor Tchesnokov tchesnok at ualberta.ca
Mon Mar 30 11:38:36 PDT 2015

Dear Elaine,

Thank you so much for the explanations! Yes, it helps a lot.


On Mon, Mar 30, 2015 at 11:50 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Egor,
> The differences are discussed in several places, for example in the
> MatchMaker manual page:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html#final
> >
> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rrdistmaps/rrdistmaps.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 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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