OK, I'm properly chastised - "outlier" does not equal "bad".
However, residues which are not flagged as problematic or unusual
during validation should not be flagged in the final pdb file.
And I have read Gerard's paper, and the molprobity paper. Recently.
Sue
On Sep 21, 2007, at 9:57 AM, Gerard DVD Kleywegt wrote:
>> Has anyone successfully fought this "bad residue" listing? I
>> understand that the pdb wishes to flag problem regions, but this
>> is not a valid way of doing so. I can tell them where the problem
>> regions are in the structure if they wish.
>
> oh dear, oh dear - touchy, touchy!
>
> coordinate-based validation (no matter which test, no matter which
> program) can only produce a list of OUTLIERS. it's up to the
> depositor or user of the model to figure out whether each
> individual outlier is an ERROR in the MODEL or a (unusual and
> possibly interesting) FEATURE of the STRUCTURE (typically by
> inspection of the density). there's no need to take the output of
> such programs as a personal insult, or to start a fight with the
> pdb, or ... [rest of diatribe mercifully deleted before hitting the
> send-button]
>
> warmly recommended review paper (really, i sometimes wonder what
> the half-life of papers on quality control and validation, and more
> generally on methods, is): http://xray.bmc.uu.se/cgi-bin/gerard/
> reprint_mailer.pl?pref=56
>
> warmly recommended tutorial (have a look at question 13 in
> particular): http://xray.bmc.uu.se/gerard/embo2001/modval/index.html
>
> --dvd
>
> ******************************************************************
> 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:[log in to unmask]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>
Sue Roberts
Biochemistry & Biophysics
University of Arizona
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