b-factor refinement

Lynn F. Ten Eyck teneyckl at sdsc.edu
Fri Mar 14 01:31:08 EST 1997

Howard Flack wrote:
> Ask Lynn van Eyck.
      Lynn Ten Eyck, actually.

There is an excellent discussion of refinement practice by Kleywegt and
Jones to come out in "Methods in Enzymology", but in the mean time
available at http://alpha2.bmc.uu.se/~gerard/gmrp/gmrp.html -- and I
strongly recommend that you download this while you can.  It doesn't so
much contain explicit cookbook advice on when to refine what as it does
advice on how to tell if what you have done is appropriate for your
data.  This is actually the correct problem to address.  The approach
relies heavily on Rfree.

The same server used to have a copy of the Kleywegt & Jones Structure
article,  Gerard J Kleywegt and T Alwyn Jones: Where freedom is given,
liberties are taken [Ways & means] Structure 1995 3 : 535-540 which has
to be one of the more enjoyable diatribes I have read in a long time. 
Alwyn and Gerard would have done very well as Old Testament prophets.

Dale Tronrud has been discussing some of these issues for a long time;
you might look at the following reference.

TRONRUD, D. E. Knowledge-based B-factor restraints for the refinement of
proteins. J. Appl. Cryst. 29, 100 (1996).

If you are going to refine your B-factors much you really must use the
bulk solvent correction and all of the low resolution data.  This has
the added bonus of making your difference maps significantly clearer.

Lynn Ten Eyck
teneyckl at sdsc.edu

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