[Biojava-l] BioJava

Andreas Prlic andreas.prlic at gmail.com
Mon Jan 12 09:28:22 UTC 2009

Hi Michal,

the code you sent looks fine to me. Still I am not sure if I fully
understand what you are trying to say. What do you mean with "each
hit" ?

>From our previous discussion I understand that you work with two sets
of atoms (residues)  where each position in one set corresponds to a
position in the other set. This means you know that all atoms are on
structurally equivalent positions and the two sets of atoms are of the
same size. If this is the case, then the SVDSuperimposer is the right
tool and you would include all atoms in the two sets for the RMSD

If you work with 2 proteins where you do NOT know the structurally
equivalent positions at the start, then StructurePairAligner provides
an algorithm to align two proteins (of different length) and find
pairs of atoms (residues) on structurally equivalent positions. In
this case, the RMSD calculation considers the positions that are
equivalent and ignores the unaligned regions. Guess I should create a
wiki page for explaining this difference between SVDSuperimposer and


2009/1/12 Michał Lorenc <m.t.lorenc at wp.pl>:
> Dear Andreas,
> I used the SVDSuperimposer class, but after Calc.rotate and Calc.shift I
> would know which Atom is close to another Atom.
> SVDSuperimposer.getRMS(caAtoms1, caAtoms2) get me only for the whole
> protein structure the RMS value, but how could I get a RMS value for
> each hit?
> I attached you my code. Thank you in advance!
> Best regards,
> Michal
> ----------------------------------------------------
> Adam Małysz na aukcji!
> Zobacz:
> http://klik.wp.pl/?adr=http%3A%2F%2Fcorto.www.wp.pl%2Fas%2F522934896.html&sid=605

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