From: Dan Wright (dtwright_at_uiuc.edu)
Date: Tue Sep 13 2005 - 09:30:02 CDT

Robin,

My understanding of the operation of STAMP (the program used to perform the
alignment) is as follows:

1) rapidly scan the (2 or more) molecules to be aligned to fit them to each
other roughly
2) progressively refine the alignment using an iterative dynamic programming
approach

In step (1), the molecules to be aligned have their coordinates shifted around
to find a starting position for performing step 2. Of course, STAMP would not
need to do this in the case of identical molecules. Hoever, since it does not
know that the molecules are identical before starting (and does not check for
identical molecules because of course it is assumed that the user wants to
align structures that differ in some respect), it still performs step 1 which,
in the case of identical structures, has the effect of un-aligning them. Step
2 then optimizes the rough alignment, but can never converge on the 100%
"perfect" solution that existed before running STAMP in the first place. You
may be able to get closer by messing with the STAMP settings before running it.

In short, STAMP was not designed for this case; it is designed to align
homologous but non-identical structures. If you do need to align identical
structures, using VMD's built-in "measure fit" command would be better. It
will fit atoms from 2 structures to each other based solely on RMSD.

Dan

Robin Bush wrote:
> 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
>
>

-- 
Dan Wright
(dtwright_at_uiuc.edu)
(http://www.scs.uiuc.edu/)
(UNIX Systems Administrator, School of Chemical Sciences, UIUC)
(333-1728)