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I'm not sure what you mean by 'ability to use harmonic restraints' - aren't
geometric restraints harmonic in all refinement programs? Atomic B-factor
not necessarily (e.g., torsion restraints can be defined with a cosine
function, and L-J-type van der Waals restraints are not harmonic) - see ye
olde (1992) x-plor manual for details
what he probably meant was *positional* harmonic restraints which can be used
to keep parts of your model close to where they are at the start of the
refinement. examples of applications are:
- to restrain monoatomic entities during cartesian MD or SA refinement - for
instance, in the old days, water molecules used to display an irritating
degree of wanderlust during SA refinement (nowadays they are kept fixed, i.e.
constrained)
- in SA-omit protocols, to prevent the bits of the model that are close to an
omitted region from wandering into density that belongs to the omitted part
- to reduce unwarranted distortions if one has a high-resolution starting
model and refines it against low-resolution data of a complex or mutant etc.
(perhaps this deserves a renaissance - see
http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=28)
--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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