Re: [ccp4bb] XDS and overlaps

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

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

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Subject: Re: XDS and overlaps
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-21

Subject: Re: XDS and overlaps
From: Michel Fodje michel {- dot -} fodje {- at -} LIGHTSOURCE {- dot -} CA
Date: 2008-02-21

I should add that inspecting the average three-dimensional profiles in
INTEGRATE.LP could give you an indication if you have overlaps or not.
The profiles look like slices through a 3D unimodal gaussian. If you
have overlaps it will be revealed by bi-/multi-modal features. However,
these are average profiles so a small number of overlaps may not be
apparent.

/Michel

On Wed, 2008-02-20 at 14:54 -0800, Engin Ozkan wrote:

> Hi everyone,
>
> 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?
>
> Thanks,
>
> Engin

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

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

Next message:
Subject: Re: XDS and overlaps
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-21