Re: [ccp4bb]: amore

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Frederico Moraes Ferreira wrote:
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> Dear All,
> Let me ask you just a little question about Amore. I have  a homodimer
> into the ASU. I tried to look for one monomer, fix it and then tried for 
> the second.
> The scores for the dimer search directly are higher and presents some 
> contrast. My question is:
> Will the highest scores always give the best solution?
> Thanks in advance
> Frederico
> 
> 


  As always - it depends... MR - easy in theory - difficult in practice!

  If you expect a homo-dimer, I would usually use it as the search 
model. However it is possible that within the crystal the dimer is 
generated by crystallographic two-fold axes, and there are in fact two 
half dimers (viz monomers!) in your asymmetric unit. Check the packing , 
and check whether your two solutions are compatible. The solutions may 
generate different symmetry mates, and be on diffeent origins. The only 
easy way to check is to generate coordinates from both solutions, and 
inspect those. the superpose task shhould match one chain from monomer 
solution to another chain of the dimer solution via a symmetry operator..

  What it might be depends on your spacegroup.

  Eleanor




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