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CCP4BB  March 2009

CCP4BB March 2009

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Subject:

Re: images

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Mon, 16 Mar 2009 09:32:53 +0000

Content-Type:

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text/plain (103 lines)

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 *
>>     *                                                             *
>>     ===============================================================
>>
>
>

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