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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?
>[...deleted...]
>> 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
>
>
>--
>/|  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
Australia
vos at biosci.uq.oz.au




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