Dear All,
I would like to inform you that two SG centers:
Center for Structural Genomics of Infectious Diseases - CSGID http://www.csgid.org
and
Seattle Structural Genomics Center for Infectious Diseases - SSGCID
http://ssgcid.org/home/Target_Status.asp
set-up the server at University of Virginia that will have diffraction images for all deposits from these two centers. Anybody in the World can have an access after simple registration.
At the moment there are only two data sets available:
3ftt - that started whole discussion
3e4f
but soon we should have all (??) of them.
Also JCSG has their server with many datasets of JCSG structures. Hopefully this policy will proliferate.
Wladek
At 11:27 AM 3/12/2009, Garib Murshudov wrote:
Dear Gerard and all MX crystallographers
As I see there are two problems.
1) Minor problem: Sanity, semantic and other checks for currently
available data. It should not be difficult to do. Things like I/sigma,
some statistical analysis expected vs "observed" statistical behaviour
should sort out many of these problems (Eleanor mentioned some and
they can be used). I do not think that depositors should be blamed for
mistakes. They are doing their best to produce and deposit. There
should be a proper mechanism to reduce the number of mistakes.
You should agree that situation is now much better than few years.
2) A fundamental problem: What are observed data? I agree with you
(Gerard) that images are only true observations. All others
(intensities, amplitudes etc) have undergone some processing using
some assumptions and they cannot be considered as true observations.
The dataprocessing is irreversible process. I hope your effort will be
supported by community. I personally get excited with the idea that
images may be available. There are exciting possibilities. For example
modular crystals, OD, twin in general, space group uncertaintly cannot
be truly modeled without images (it does not mean refinement against
images). Radiation damage is another example where after processing
and merging information is lost and cannot be recovered fully. You can
extend the list where images would be very helpful.
I do not know any reason (apart from technical one - size of files)
why images should not be deposited and archived. I think this problem
is very important.
regards
Garib
On 12 Mar 2009, at 14:03, Gerard Bricogne wrote:
Dear Eleanor,
That is a useful suggestion, but in the case of 3ftt it would
not have
helped: the amplitudes would have looked as healthy as can be (they
were
calculated!), and it was the associated Sigmas that had absurd
values, being
in fact phases in degrees. A sanity check on some (recalculated) I/ sig(I)
statistics could have detected that something was fishy.
Looking forward to the archiving of the REAL data ... i.e. the
images.
Using any other form of "data" is like having to eat out of someone
else's
dirty plate!
With best wishes,
Gerard.
--
On Thu, Mar 12, 2009 at 09:22:26AM +0000, Eleanor Dodson wrote:
It would be possible for the deposition sites to run a few simple
tests to
at least find cases where intensities are labelled as amplitudes or
vice
versa - the truncate plots of moments and cumulative intensities at
least
would show something was wrong.
Eleanor
--
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* Gerard Bricogne g...@globalphasing.com *
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* Global Phasing Ltd. *
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===============================================================
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:
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University of Virginia
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