Hi
I'm afraid the adoption of imgCIF (or CBF, its useful binary
equivalent) doesn't help a lot - I know of three different
manufacturers of detectors who, between them, write out four different
image formats, all of which apparently conform to the agreed IUCr
imgCIF standard. Each manufacturer has its own good and valid reasons
for doing this. It's actually less work for me as a developer of
integration software to write new code to incorporate a new format
than to make sure I can read all the different imgCIFs properly.
On 16 Mar 2009, at 09:32, Eleanor Dodson wrote:
The deposition of images would be possible providing some consistent
imagecif format was agreed.
This would of course be of great use to developers for certain
pathological cases, but not I suspect much value to the user
community - I down load structure factors all the time for test
purposes but I probably would not bother to go through the data
processing, and unless there were extensive notes associated with
each set of images I suspect it would be hard to reproduce sensible
results.
The research council policy in the UK is that original data is meant
to be archived for publicly funded projects. Maybe someone should
test the reality of this by asking the PI for the data sets?
Eleanor
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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--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 0QH
