Re: [ccp4bb] XDS and overlaps

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CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008

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Subject: Re: XDS and overlaps
From: Petri Kursula pkursula {- at -} SUN3 {- dot -} OULU {- dot -} FI
Date: 2008-02-22

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Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Ulrich Baumann ulrich {- dot -} baumann {- at -} IBC {- dot -} UNIBE {- dot -} CH
Date: 2008-02-22

Subject: Re: XDS and overlaps
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-02-22

Dear all,

I've written
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/INTEGRATE
hoping that this will explain how XDS works (the last part focuses on
the overlap question). Caveat: this is written to the best of my knowledge.

I would also like to draw your attention to the article "Quality
Control" in XDSwiki. This would benefit _a_ _lot_ if people who have/had
problems with data from XDS could donate their raw data (to be put on
our FTP server, like the PulG data), with the goal of having a proper
data reduction (pinpointing and solving problems!) and evaluation in the
wiki. I believe that by moving from "anecdotal evidence" and "hearsay"
to an evidence-based evaluation of algorithms (with publicly accessible
data), everybody would benefit.

best,

Kay

Engin Ozkan schrieb:
> In this case, XDS-processed data is clearly twinned, if one were to
> believe moments and the cumulative intensity distribution calculated by
> truncate (and everyone should - channelling Dr. Dodson).
>
> Why I'm worried about XDS separating relatively overlapped spots is the
> funny intensity stats that may result from this (as George Sheldrick and
> Martin Hallberg has pointed out)? The incomplete HKL2000-processed data
> (70%) still has intermediate values for the intensity stats, leaning
> towards twinning. This somewhat agrees with twinning, but not
> overzealous data integration.
>
> Engin
>
> P.S. If twinning (perfect in this case) is taken into account structure
> refines to 20/26% R at 2.8 Ang., unlike in Martin's case. Without
> twinning, numbers are 29/33%.
>
> Quoting "George M. Sheldrick" :
>
>> All SHELX programs and XPREP are also indifferent to the asu choice
>> and to whether the data have been merged or not (even SHELX-76). It
>> is CCP4 historical baggage and high time it was eliminated.
>>
>> On the official thread of this discussion, my impression is that 3D
>> integration programs (like XDS) are able to handle overlapping
>> reflections better than 2D integration programs, as one would expect.
>> One simple test is the mean value of
E^2-1
; if is is too small,
>> you either have twinning or reflection overlap. Unfortunately and
>> surprisingly XDS often fails this test (especially if the data have
>> been flattened with XSCALE),
>>
>> George
>>
>> On Thu, 21 Feb 2008, Peter Zwart wrote:
>>
>>>
>>> or use phenix, which is indifferent to format and asu choice.
>>>
>>>
>>> P
>>>
>>
>> Prof. George M. Sheldrick FRS
>> Dept. Structural Chemistry,
>> University of Goettingen,
>> Tammannstr. 4,
>> D37077 Goettingen, Germany
>> Tel. +49-551-39-3021 or -3068
>> Fax. +49-551-39-2582
>>

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CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008

Previous message:
Subject: Re: XDS and overlaps
From: Petri Kursula pkursula {- at -} SUN3 {- dot -} OULU {- dot -} FI
Date: 2008-02-22

Next message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Ulrich Baumann ulrich {- dot -} baumann {- at -} IBC {- dot -} UNIBE {- dot -} CH
Date: 2008-02-22