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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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