PS I wasn't aware Nature now requires structure factors to be
submitted - which breaks down one of my arguments...
I still hope the authors provide the images though, otherwise I will
start suspecting much more structure than I do now.
In the meantime, all for required submission of raw images, both to
prevent misconduct and to help program developers.
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
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/
On 16 Aug 2007, at 17:59, Eleanor Dodson wrote:
This structure (1h6w) provides an interesting comparison; it looks
just as I would expect though for such an interesting extended fold.
There are big peaks on the 3-fold axis; there is wispy density
which would be very hard to model - I found an ILE in the wrong
rotamer (341A) - (there is ALWAYS something you can improve) - in
other words it looks like a real map..
And the intensity plots look as expected too..
Eleanor
Mark J. van Raaij wrote:
Dear all,
With regards to the possible "fabrication" of the 2hr0 structure,
why would the authors have deposited the structure factors if this
is not required by the journal? Also, why would they have
"fabricated" a structure with gaps along c if they could have done
so without the gap?
I few years ago, I had to cope with two structures with gaps along
c, pdb codes 1h6w and 1ocy those of you who are interested,
structure factors are available from the pdb, unmerged intensities/
raw images I will look for and provide if requested...
Without further evidence, I suspect their structure is real,
perhaps not optimally refined and treated though, but then again,
this seems commonplace in "Nature" structures, perhaps due to lack
of time/experience and, in some cases, putting too much pressure
on the PhD students/postdocs involved instead of mentoring and
checking them. I hope the authors provide the raw diffraction
images to dispel any doubts and would be curious to learn about
the other structures of the same group - anyone has a
comprehensive, annotated list of them?
Greetings,
Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/ <http://web.usc.es/%7Evanraaij/>
On 16 Aug 2007, at 15:22, Randy J. Read wrote:
On Aug 16 2007, Eleanor Dodson wrote:
The weighting in REFMAC is a function of SigmA ( plotted in log
file).
For this example it will be nearly 1 for all resolutions ranges
so the weights are pretty constant. There is also a contribution
from the "experimental" sigma, which in this case seems to be
proportional to |F|
Originally I expected that the publication of our Brief
Communication in Nature would stimulate a lot of discussion on
the bulletin board, but clearly it hasn't. One reason is probably
that we couldn't be as forthright as we wished to be. For its own
good reasons, Nature did not allow us to use the word
"fabricated". Nor were we allowed to discuss other structures
from the same group, if they weren't published in Nature.
Another reason is an understandable reluctance to make
allegations in public, and the CCP4 bulletin board probably isn't
the best place to do that.
But I think the case raises essential topics for the community to
discuss, and this is a good forum for those discussions. We need
to consider how to ensure the integrity of the structural
databases and the associated publications.
So here are some questions to start a discussion, with some
suggestions of partial answers.
1. How many structures in the PDB are fabricated?
I don't know, but I think (or at least hope) that the number is
very small.
2. How easy is it to fabricate a structure?
It's very easy, if no-one will be examining it with a suspicious
mind, but it's extremely difficult to do well. No matter how well
a structure is fabricated, it will violate something that is
known now or learned later about the properties of real
macromolecules and their diffraction data. If you're clever
enough to do this really well, then you should be clever enough
to determine the real structure of an interesting protein.
3. How can we tell whether structures in the PDB are fabricated,
or just poorly refined?
The current standard validation tools are aimed at detecting
errors in structure determination or the effects of poor
refinement practice. None of them are aimed at detecting specific
signs of fabrication because we assume (almost always correctly)
that others are acting in good faith.
The more information that is available, the easier it will be to
detect fabrication (because it is harder to make up more
information convincingly). For instance, if the diffraction data
are deposited, we can check for consistency with the known
properties of real macromolecular crystals, e.g. that they
contain disordered solvent and not vacuum. As Tassos Perrakis has
discovered, there are characteristic ways in which the standard
deviations depend on the intensities and the resolution. If
unmerged data are deposited, there will probably be evidence of
radiation damage, weak effects from intrinsic anomalous
scatterers, etc. Raw images are probably even harder to simulate
convincingly.
If a structure is fabricated by making up a new crystal form,
perhaps a complex of previously-known components, then the
crystal packing interactions should look like the interactions
seen in real crystals. If it's fabricated by homology modelling,
then the internal packing is likely to be suboptimal. I'm told by
David Baker (who knows a thing or two about this) that it is
extremely difficult to make a homology model that both obeys what
we know about torsion angle preferences and is packed as well as
a real protein structure.
I'm very interested in hearing about new ideas along these lines.
The wwPDB has agreed to sponsor a workshop next year where we
will propose and test new validation criteria.
4. If new validation criteria are applied at the PDB, won't
someone who wants to fabricate a structure just keep improving
their fabricated model until it passes all the tests?
That's a possibility, but I think the deterrence effect of
knowing that there are measures to detect fabrication will
outweigh this. And it isn't enough for a fabricated structure to
pass today's tests; it has to pass all the new tests devised for
the rest of the person's life, or at least their career.
5. What should we do if tests suggest that a structure may be
fabricated?
I think we need to be extremely careful. Conclusions should not
be drawn on the basis of a few numbers. The tests can just point
up which structures should be examined closely. Close examination
would then involve less automated criteria, such as whether the
structure agrees with all the biochemical data about the system.
As in the process followed by Nature, you also have to start by
giving the people who deposited the structure an opportunity to
explain the anomalies.
Randy Read