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Re: [ccp4bb]: Equivalence in Structural alignments



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Iain Kerr wrote:
> 
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> Following on from the recent bb discussion on 'Structure-based sequence
> alignment', I am wondering how one would decide whether or not two residues
> are 'structurally equivalent' between two superimposed molecules if they
> are not obviously sitting on top of one another. The regions I am concerned
> with have the same number of residues in each molecule, so no obvious
> insertions. Is there a consensus about the minimium distance between  two
> potentially equivalent positions or is it just a case of making a decision
> and sticking with it.
> 


 Doesnt this have to be problem driven - eg. if you are trying to argue
the a catalytix triad is equivalent to another you need the H bonding
etc atoms very close indeed, but the CAs might be As away..

 But if you are comparing globin helices you expect most of the CAs to
be with 0.5A I guess..

 Just trying to muddy the waters!

  Eleanor