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B-factor refinement in v3.1 vs v3.851

Siska vos at biosci.uq.edu.au
Tue Dec 9 02:25:28 EST 1997

>At 9:14 PM -0800 on 12/4/97 you (Siska Vos) suggested:
>> Dear All,
>> Has anyone experienced differences in B-factor refinement depending on
>> whether Xplor v3.1 or Xplor v3.851 is used?
>> I use the brefinement.inp files recommended for each Xplor version and
>> the parameter files specified within these correspond to those for
>> v3.851.  The weights, resolution range, sigma cutoff, etc are the same
>> in both.
>> The Fo-Fc map produced for the v3.851 refined model is much noisier,
>> with a large negative peak over the substrate molecules.  This is
>> presumably because v3.851 does not refine B-factors to values above 100.
>> However, the 2Fo-Fc map for this model is slightly better, particularly
>> for two other ligands bound to the protein.
>This sounds like you may be having a problem that has bitten a few
>people here recently.  Check your atom types in your cofactor topology
>files, then check to see if the $XTALLIB:scatter.lib file supplied with
>Xplor v3.851 has entries which are not what you might want or expect.
>We've had problems with things like 'NP' (became "neptunium" instead of
>"pyrole nitrogen") and 'OS' (became "osmium" instead of "phospho-ester
>oxygen").  Both of these problems came when using the topology files
>supplied with Xplor v3.851 (for heme and fmn, respectively).
>I've avoided that particular problem by creating my own scattering
>libarary with just the atomtypes that I expect to be present in my
>structure.  I do the same thing with the spacegroups--I'm afraid that
>in a file that big, there's at least one typo, and Murphy's law says
>that it will happen to me.
>Hope that you get things cleared up.
>/|  John D. Barton
>\|  Department of Biochemistry and Molecular Biophysics
>/|> Washington University School of Medicine
>\|> email: John.Barton at pobox.com

Thank you very much for your suggestion!  It turns out that one of the
purine ring carbon atoms, which is named CE, becomes a "cerium" atom.  I
have repeated the B-factor refinement in v3.851, including the necessary
scattering factors only, and the B-factors for the substrate now match
those from v3.1.

Thank you again for your help.

Siska Vos
Centre for Drug Design and Development
The University of Queensland
vos at biosci.uq.oz.au

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