Re: advice on rmsd algorithms....
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hi Jay, probably the alignments are not the same. Did you look at the results in 3D and does the MolMol alignment make any sense? Andreas On Mon, Jan 24, 2011 at 1:38 PM, Jay Vyas <[email protected]> wrote: > Hi guys . I noticed that I get a different RMSD using the biojava alignCE > methd, (CeMain), as compared to MolMol, another popular molecular > visualization tool. > > Any idea why ? The rmsd appears to be 2.54 (biojava CEMain) as compared to > 13.5 (molmol). Im using the gap size of -1 as in the biojava > examples..... > > > > -- > Jay Vyas > MMSB/UCHC > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l