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On Oct 11, 2006, at 1:49 PM, Santarsiero, Bernard D. wrote:
the graphics program "O" is excellent at things like this.
Basically you
do a rough superposition with lsq-exp (explicit) and then improve
it with
lsq-imp. It leaves out calpha's that aren't close, but pulls
everything
else in.
Yes, the way that O does it with lsq is much preferred over many
other methods. However, it really is just a kludge to overcome the
problems with least-squares, an optimization method that really is
inappropriate for the macromolecular superposition problem. The
advantage of the maximum likelihood method that THESEUS implements,
is that it removes the arbitrary and subjective parameters for
deciding what "isn't close". Maximum likelihood instead inherently
down-weights the variable parts exactly by the (statistically) proper
amount.
Additionally, lsq does not do a bona fide simultaneous superposition
with more than two structures, whereas THESEUS does.
Cheers,
Douglas
Bernie Santarsiero
On Wed, October 11, 2006 10:38 am, Douglas L. Theobald wrote:
On Oct 11, 2006, at 11:08 AM, Jenny wrote:
Hi, All,
I have three proteins that only differ in one big loop(resi
46-59).So I'm trying to superimpose three proteins and keep the
same part fixed.( basically, superimpose by residue 1-45 and
residue 60-120).Is there easy way to do this?
Hi Jenny,
It's easy to do with THESEUS from the command line:
http://www.theseus3d.org/
For a least squares fit, just use something like:
theseus -l -s1-45:60-120 protein1.pdb protein2.pdb protein3.pdb
or equivalently, exclude the range with:
theseus -l -S46-59 protein1.pdb protein2.pdb protein3.pdb
However, since THESEUS uses maximum likelihood you shouldn't even
have to specify a residue range, just do:
theseus protein1.pdb protein2.pdb protein3.pdb
and it should work well.
^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
Douglas L. Theobald
Department of Biochemistry
Brandeis University
Waltham, MA 02454-9110
[EMAIL PROTECTED]
GPG key ID: 38E9EB53
https://www.molevo.org/keys/38E9EB53.gpgkey
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