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
>>>>
>>>
>>>
>>> --
>>>
>>> ===============================================================
>>> * *
>>> * Gerard Bricogne [log in to unmask] *
>>> * *
>>> * Global Phasing Ltd. *
>>> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
>>> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
>>> * *
>>> ===============================================================
>>>
>>
>>
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 0QH
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