On 17/10/2011 01:52, Wladek Minor wrote:
Frank,
This is serious problem for biologists. There is a structure with
ligand. The same data were re-interpreted and people did not find the
ligand. This re-interpretation is not really valid until we will look
into diffraction data. Biologist lost tremendous amount of time and
effort looking into interfratation and ...
NOw this is very important biomedical structure.
Yes I know and agree partially.
That said: I reckon we vastly overestimate the value of individual
structures; it's the ensemble that is informative. A decade from now,
depositing a single structure of a protein will be seen to be as just as
silly as it is currently not to deposit structure factors.
Including those "very important biomedical structures". Those things
tend to become suddenly "important" (in the grand scheme) only after the
ligand's biological/clinical effects could be demonstrated. And even
then the structure itself is only important if it helps a chemist.
If this sounds extreme: consider how much other data it now takes to
get structures into nature/science/cell. Or what happened (or rather
didn't) to all those patents on structures that were such a big deal a
decade ago.
phx.
Wladek
At 02:59 PM 10/16/2011, you wrote:
One other question (for both key issues described): what exactly is
the problem the committees are aiming to address?
Because I can't help noticing that Tom's email did not spark an
on-list discussion; do people actually feel either are issues?
Isn't the more burning problem how best to use the 10,000s of
structures we're churning out? In the grand scheme of things,
they're pretty inaccurate anyway:
static snapshots of crippled fragments of proteins far from their
many interaction partners. So do we need 100,000s of structures
instead? If so, we may soon (collectively) stop being able to care
about the original dataset or how to reproduce analysis number 2238
from 2 years ago.
(No, I'm not convinced this question is relevant only to structural
genomics.)
phx.
On 16/10/2011 19:38, Frank von Delft wrote:
On the deposition of raw data:
I recommend to the committee that before it convenes again, every
member should go collect some data on a beamline with a Pilatus
detector [feel free to join us at Diamond]. Because by the probable
time any recommendations actually emerge, most beamlines will have
one of those (or similar), we'll be generating more data than the
LHC, and users will be happy just to have it integrated, never mind
worry about its fate.
That's not an endorsement, btw, just an observation/prediction.
phx.
On 14/10/2011 23:56, Thomas C. Terwilliger wrote:
For those who have strong opinions on what data should be deposited...
The IUCR is just starting a serious discussion of this subject. Two
committees, the "Data Deposition Working Group", led by John Helliwell,
and the Commission on Biological Macromolecules (chaired by
Xiao-Dong Su)
are working on this.
Two key issues are (1) feasibility and importance of deposition of raw
images and (2) deposition of sufficient information to fully
reproduce the
crystallographic analysis.
I am on both committees and would be happy to hear your ideas
(off-list).
I am sure the other members of the committees would welcome your
thoughts
as well.
-Tom T
Tom Terwilliger
terwilli...@lanl.gov
This is a follow up (or a digression) to James comparing test set to
missing reflections. I also heard this issue mentioned before
but was
always too lazy to actually pursue it.
So.
The role of the test set is to prevent overfitting. Let's say I have
the final model and I monitored the Rfree every step of the way
and can
conclude that there is no overfitting. Should I do the final
refinement
against complete dataset?
IMCO, I absolutely should. The test set reflections contain
information, and the "final" model is actually biased towards the
working set. Refining using all the data can only improve the
accuracy
of the model, if only slightly.
The second question is practical. Let's say I want to deposit the
results of the refinement against the full dataset as my final model.
Should I not report the Rfree and instead insert a remark
explaining the
situation? If I report the Rfree prior to the test set removal,
it is
certain that every validation tool will report a mismatch. It
does not
seem that the PDB has a mechanism to deal with this.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is
crazy?
Julian, King of
Lemurs
Dr. Wladek Minor
Professor of Molecular Physiology and Biological Physics
Phone: 434-243-6865
Fax: 434-982-1616
http://krzys.med.virginia.edu/CrystUVa/wladek.htm
US-mail address:
Department of Molecular Physiology and Biological Physics
University of Virginia
PO Box 800736, Charlottesville, VA 22908-0736
Fed-Ex address:
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University of Virginia
Charlottesville, VA 22908
