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[ccp4bb]: Equivalence in Structural alignments



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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.

As always, thanks in advance for any help.

Iain



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                       Iain Kerr
     Biomolecular Sciences Building,
                      3rd floor,                            
                 North Haugh,                        
                  St.Andrews, 
              The University,
              Fife KY16 9ST,                      
                Scotland, UK.       

        phone: +44 (0)1334 467265 

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