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 calculation. 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 StructurePairAligner... Andreas 2009/1/12 Michał Lorenc <[email protected]>: > 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
