OK, so there are two things -- sequence alignment (which obviously this is
not) and then structural superposition based on some sort of selected
criteria. I'm having a bit of trouble seeing why that second stage is not
the "structural alignment" part -- you're sure of that? What other functions
are generally done at that stage? (Is that when atom pairing is adjusted, or
is atom pairing not part of that yet?)
I should point out that Jmol is not technically atom-pairing at all. It is
definitely pairing residues (any pairing the user desires is available), but
it doesn't ever work at the atom-pairing level.
Be that as it may, I'm also quite happy to change the name to anything
reasonable. Since it's not just doing (at this point) a standard
matrix-based RMSD minimization operation (which is what you want to call a
superposition, I think), I know I have to be careful with whatever I call
it.
It may sound strange, but what Jmol is doing is minimizing the
four-dimensional "distance" between the two structures in terms of
orientation. The actual "superposition" is just a translation after that.
Suggestions!
Bob
On Mon, Mar 15, 2010 at 1:30 PM, <[email protected]> wrote:
> On Mon, 15 Mar 2010 11:29:40 -0500, Robert Hanson <[email protected]>
>
> [snip]
>
> >
> > The operation Jmol is performing is definitely an alignment of sorts; I
> can
> > certainly be careful not to claim it is "structural" alignment if that
> term
> > is now synonymous with something more involved.
>
> "of sorts"
>
> It really is a superposition or, as Mercury names it:
>
> a structure overlay (when doing a pair-wise fit with at least one pair of
> equivalent atoms designated)
>
> a molecule overlay (when two molecules with the same number of atoms are
> used)
>
> For example, for an asymmetric unit with two independent atoms just select
> one atom in each (without having to pick the equivalent atom in each) and
> ask the program to do the overlay (superposition).
>
> Rich
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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