Andreas,
Possibly. PyMol calls it structural alignment and uses the same command
name.
http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/
While I haven't implement that standard technique of minimization of
coordinate RMSD, the "align" command is set up to that if people are
interested in that and thus do precisely what PyMol does. But in addition,
the command allows a different sort of minimization -- orientational
(quaternion) minimization. I'm not sure any other program implements that,
and the idea here is to allow us to find out how it performs. Right now this
is what I have implemented because that is my interest and, it turns out,
almost trivial to implement.
But I see your point - -that true "structural alignment" is something far
more involved. Particularly if there are no pair-wise residue correlations.
So I'm guessing you would have the same complaint about the PyMol command.
Yes?
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.
Bob
--
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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