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:[EMAIL PROTECTED]
******************************************************************
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
[EMAIL PROTECTED]
