Dear all,
I agree with MM about the ligand and complex structures. Even in the
most honest circumstances, it is easy to get carried away with hopes and
excitement. My personal embarassing experience was some years ago. It
involved a protein that I had crystallized in a different space group in
the
-Original Message-
From: Kantardjieff, Katherine
[mailto:[EMAIL PROTECTED]
Sent: Friday, August 17, 2007 4:55 PM
To: [EMAIL PROTECTED]; Dale Tronrud
Subject: RE: [ccp4bb] The importance of USING our validation tools
Since my name appeared in this email exchange, I thought I should
respond
The literature already contains quite a few papers discussing ligand-protein
interactions derived from low-resolution data, noisy data, etc. It's
relatively easy to take a low-quality map; dock the molecule willy-nilly
into the poorly defined 'blobule' of density, and derive spectacular
conclusions
To complete your analogy to the "ORTEP of the year", the summary page could be
accompanied by a backbone ribbon drawing of the macromolecule, with a red
sphere at each residue that has an error. You could get fancy and scale the
sphere according to the severity of the error.
-Tom
-Or
Hi Mischa,
I think you are right with ligand structures and it would be very
difficult if not impossible to distinguish between real measured data
and faked data. You just need to run a docking program dock the ligand
calculate new structure factors add some noise and combine that with
your r
I agree. However, I am personally not so much worried about entire protein
structures being wrong or fabricated. I am much more worried about
co-crystal structures. Capturing a binding partner, a reaction
intermediate or a substrate in an active site is often as spectacular an
achievement as de
I wholeheartedly agree with George!
A single-page summary of any given PDBID, with some of the less obvious
warnings/error codes explained at the bottom, would speak volumes to almost
any reviewer - and as George pointed out it's very unlikely that reviewers
will bother to look at diffraction imag
There are good reasons for preserving frames, but most of all for the
crystals that appeared to diffract but did not lead to a successful
structure solution, publication, and PDB deposition. Maybe in the future
there will be improved data processing software (for example to integrate
non-merohe
it is still very bad, but at least it would mean there was some
experimental
evidence for the model and it was not completely made up.
Mark
Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
