If I am right, the Pymol align command does a sequence alignment followed by
a superposition of atoms.
http://www.pymolwiki.org/index.php/Align
I am not a big friend of naming discussions, just trying to help avoid
future questions ... ;-)
Andreas
On Mon, Mar 15, 2010 at 9:29 AM, Robert Hanson <[email protected]> wrote:
> 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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