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Does anybody know how to include phi/psi dihedral restraints to minimization
or torsion annealing in CNS? Many Thanks
you have to ask yourself if you really, really, really want to do that. and if
the answer is 'yes' you have to ask yourself again
the reason is that the conformational torsion angles are eminently suited for
validation purposes, but only when they are unrestrained. in other words, once
you restrain phi and psi, you can't use ramachandran plots any longer (well,
you can, but they are useless as validation tools)
if you still want to do it, there are two ways i can think of. one is to use
the database-derived torsion restraints of kuszewski and clore - these used to
be in xplor, not sure about cns. however, this is not recommended until the
model is nearly finished because these restraints tend to pull your residues
into the *nearest* well of the 'ramachandran energy' which is not necessarily
the same as the *correct* well
the other method is to restrain the torsions in your new crappy 3 A model to
the values they had in your bright and shining 1.5 A model. you can use XPLO2D
to generate the restraints file which you can include into your xplor script
(and i reckon it should work with cns as well). for a description, see:
http://xray.bmc.uu.se/usf/xplo2d_man.html#H5
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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