VMD-L Mailing List

From: Robin Bush (rmbush_at_uci.edu)
Date: Fri Sep 09 2005 - 12:57:24 CDT

Hi,

If you load identical copies of a molecule, then do a structural
alignment and calculate the RMSD per residue, the resulting values,
while small, are not all zero.

Can anyone tell me why?

All I did was copy a pdb file, then load both the original and the
copy, and click away as follows...

VMD Main -> Extensions -> Analysis -> Multiple Alignment
Multiple Alignment -> Alignment -> Run Structural Alignment
Multiple Alignment -> Tools -> RMSD Tools -> RMSD Per Residue

Thanks,

Robin