> 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
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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]
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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