[Biojava-l] advice on rmsd algorithms....

[Andreas Prlic]

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 <jayunit100 at gmail.com> 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
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>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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