Re: [ccp4bb] XDS and overlaps

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Subject: Re: XDS and overlaps
From: Martin Hallberg Martin {- dot -} Hallberg {- at -} KI {- dot -} SE
Date: 2008-02-21

Hi,
Going back to your original question regarding integration with XDS.

On Feb 20, 2008, at 11:54 PM, Engin Ozkan wrote:
>
> I have been recently relying on XDS quite a bit, but at the same
> time worrying about how XDS treats overlaps. We had one dataset
> that both HKL2000 and Mosflm would show to have severe overlaps, as
> expected due to unit cell parameters and the unfortunate crystal
> orientation in the loop. We always ended up with completeness
> percentages in the 70's.
>
> XDS can find the same lattice, index and scale the data, but yields
> a 100% complete mtz (and a nice structure). Without the HKL/Mosflm-
> like GUI, it is difficult to assess the fate of the overlapped
> observations in XDS. What I could see with VIEW was that some
> observations were being divided into several ovals, probably
> different reflections, but I'm not very certain.
>
> So, the basic question is, how does XDS treat overlaps? I could not
> find in the documentation an answer to this question; the single
> mention of overlaps I could find tells me that XDS can recognize
> overlaps, but does not tell me if it rejects them, or divvies them
> up into separate reflections, and if that is the case, how does it
> divide them, and how reliable is that? Depending on how it divides
> the overlaps, could that affect commonly-used intensity stats and
> distributions?

One answer lies in the XDS 3D profiles (already been pointed out by
Kay and Bernard).
But XDS at least used to be quite liberal with inclusion of overlaps
and we had one case quite a while
back where Mosflm/DENZO would say ~40% overlaps while XDS happily
integrated everything
and delivered a complete dataset. The cumulative intensity
distribution of this dataset looked "strange"
(would love to give you a screenshot but I can't get hold of that old
data in an instant) and the structure didn't refine well.
Of course, the dataset should never have been collected like this (and
no, I was not guilty) but that was
what we had and crystals couldn't be repeated at that time.

What worked in the end was to use the DENZO predictions and integrate
it using PrOW which
performs deconvolution of spatially overlapped spots. After this the
cumulative intensity distribution
looked normal and the structure refined well.

Reference to PrOW:
Acta Crystallogr D Biol Crystallogr. 55,1733-41.
"New processing tools for weak and/or spatially overlapped
macromolecular diffraction patterns."
by Dominique Bourgeois.
Link: http://scripts.iucr.org/cgi-bin/paper?BA0019

Best regards,

Martin

.
B. Martin Hallberg, PhD
Assistant professor
Department of Cell and Molecular Biology
Medical Nobel Institute
Karolinska Institutet
Nobels v. 3
SE-171 77 Stockholm
Sweden

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CCP4bb <-- 2008 <-- February 2008 <-- 21 February 2008

Previous message:
Subject: Re: Vista
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2008-02-21

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Subject: Re: Tough Low-Res MR
From: Chavas Leo ccp4hnaalas {- at -} GMAIL {- dot -} COM
Date: 2008-02-21