[ccp4bb] images

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 3ftt and gremlins
From: Wladek Minor wladek {- at -} IWONKA {- dot -} MED {- dot -} VIRGINIA {- dot -} EDU
Date: 2009-03-12

Next message:
Subject: Re: Update X11 in macbook
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2009-03-12

Subject: images
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-03-12

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 gb10@GlobalPhasing.com *
> * *
> * Global Phasing Ltd. *
> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
> * *
> ===============================================================
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 3ftt and gremlins
From: Wladek Minor wladek {- at -} IWONKA {- dot -} MED {- dot -} VIRGINIA {- dot -} EDU
Date: 2009-03-12

Next message:
Subject: Re: Update X11 in macbook
From: Andreas_Förster docandreas {- at -} GMAIL {- dot -} COM
Date: 2009-03-12