Dear Andreas, Thanks for your answer. I saw the run of the example you had linked. As I found, all rmsd numbers which were calculated in the example were related to Local Alignments. Wheares I need to find the RMSD of Global Alignment (without any Gap). And we should consider all Alpha Carbons of the proteins to calculate the RMSD. Which parameters should I change in align method to reach the Global Alignment with NO Gap? Thanks again, ArmitaSh
--- On Thu, 12/25/08, Andreas Prlic <[email protected]> wrote: From: Andreas Prlic <[email protected]> Subject: Re: [Biojava-dev] How can I calculate the RMSD of Global Alignment? To: [email protected] Cc: "Biojava" <[email protected]>, "biojava-dev" <[email protected]> Date: Thursday, December 25, 2008, 7:20 PM Hi Armita, I agree the missing documentation for all the alignment parameters is a problem... It is not exactly clear from your mail what is the problem you encountered. The code that you sent in principle looks fine. I suspect you want to select the "best" of the alternative alignments? In that case you can simply take the first, since the alignments come out sorted. An example can be run from here: http://www.biojava.org/download/performance/biojava-structure-example1.jnlp The alternative alignments are sorted according to their number of structurally equivalent residues. The rmsd in the different alternative solutions is always kept under a certain threshold (one of the parameters), since one of the strategies is to try to keep the rmsd constant, while maximizing the number of structurally equivalent residues. Similar results are clustered together in the same cluster. In the example shown above this allows to find the multiple matches between the four chains of hemoglobin and myoglobin. Andreas On Wed, Dec 24, 2008 at 6:02 PM, Armita Sheari <[email protected]> wrote: > Hi everyone, > > I want to calculate the RMSD relevent to the Structural Global Alignment of two proteins. I have used the align method of the StructurePairAligner class with default parameters, and then I have calculated the RMSD using the getRmsd method of the AlternativeAlignment class. But it seems something is wrong. > I think I should change some parameters of align method which are defined in StrucAligParameters class. Unfortunately, I couldn't find any documentation that describes the parameters (not in the api nor in the source code). > > I would be thankful if you take a look at my code and let me know your opinion about which parameter(s) I should change. > > StructurePairAligner structurePairAligner = new StructurePairAligner(); > structurePairAligner.align(structure1, structure2); > AlternativeAlignment[] alternativeAlignment = structurePairAligner.getAlignments(); > ClusterAltAligs.cluster(alternativeAlignment); > > double minRmsd = 1000; > double rmsd = 0; > for(int i = 0; i < alternativeAlignment.length; i++) > { > rmsd = alternativeAlignment[i].getRmsd(); > if(rmsd < minRmsd) minRmsd = rmsd; > rmsd = 0; > } > return minRmsd; > > Thanks, > Armitash > > > > > > > > _______________________________________________ > biojava-dev mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-dev > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
