Hi Jay, what are the pdb Ids? When I try this for e.g. 4hhb.A against itself I am getting an RMSD of 0.
Use the afpChain.getTotalRmsdOpt() to get the RMSD of the final alignment. (see also DemoCE.java) Andreas On Wed, Jun 22, 2011 at 3:24 PM, Jay Vyas <[email protected]> wrote: > Hi guys.. Im finding that two structures that are the same give me non-zero > RMSD alignments.... There could be a bug in my code, but this is an > initial notice that I'm pretty sure about.... Any thoughts on the > performance of CEAlign in ideal cases ? > > > Atom[] ca1 = GPdbUtils.getAtoms(s1, type); > Atom[] ca2 = GPdbUtils.getAtoms(s2, type); > > System.out.println("Aligning two sets of atoms, " + ca1.length > +","+ca2.length); > // get default parameters > CeParameters params = new CeParameters(); > > // set the maximum gap size to unlimited > // params.setMaxGapSize(-1); > StructureAlignment algorithm = StructureAlignmentFactory > .getAlgorithm(CeMain.algorithmName); > > // The results are stored in an AFPChain object > AFPChain afpChain = algorithm.align(ca1, ca2, params); > afpChain.setName1("A"); > afpChain.setName2("B"); > > return (float) afpChain.getChainRmsd(); > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
