Re: [ccp4bb] XDS and overlaps -cumulative intensity distributions, E-test

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Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-22

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From: Jordi Benach jbenach {- at -} CELLS {- dot -} ES
Date: 2008-02-22

Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-02-22

Hi Clemens,

Clemens Vonrhein schrieb:
> Hi Kay,
>
> On Fri, Feb 22, 2008 at 10:18:26AM +0100, Kay Diederichs wrote:
>>> By the way, I think a part of the problem may also arise that CORRECT or
>>> XSCALE apply too many correction factors -- try CORRECTIONS=DECAY only.
>>> Gives worse R-factors and worse I/sig(I) but sometimes nicer intesity
>>> distributions.
>> Sorry, have to disagree. Just look at e.g. MODPIX.pck and you know why
>> the MODULATION correction is needed. The detectors are unfortunately not
>> ideal.
>
> True - if the correction leads to perfect data. I could see cases
> where _not_ doing the corerction can be beneficial though: the
> reflections in the non-ideal areas of the detector are kept in so bad
> shape, that the scaling/merging step remove them as outliers (keeping
> good symmetry-related copies of those reflections in). This might be
> better than having a partially corrected reflection in the dataset
> that fails the outlier-rejection test and then adds additional noise
> to e.g. a small anomalous difference.

Unlikely: XDS does not correct in the outer areas of the detector that
have no reflections above MINIMUM_I/SIGMA= (default 3). And it needs
REFLECTIONS/CORRECTION_FACTOR= (default 50) of these. By VIEWing
MODPIX.pck you can see where on the detector corrections are made.

>
> But in general I agree: these corrections in CORRECT work quite well
> and one should always start with the defaults (as with all other
> software: the authors usually have a pretty good idea and reason why a
> default is what it is).
>
> If the structure doesn't refine well or isn't solved fully
> automatically, there is always a possibility and go back to the
> integration and change those defaults. E.g. the default in XDS is to
> not refine any parameters during the INTEGRATE step: this can also be
> changed I guess to follow e.g. changes in distance (misaligned
> crystal), detect cell change due to radiation damage etc etc.
>
> Cheers
>
> Clemens
>

I can only add to this:
- as always, if you know what you're doing you can sometimes get better
data by changing parameters from their defaults
- this is one of the reasons to start XDSwiki - if all data, programs
and defaults were perfect there would not be a real reason
- the user is strongly advised to read (and think about) the .LP files,
as well as to inspect (with VIEW) the .pck files written by XDS. This,
too, is not different from any other piece of fairly complex software.

Kay

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Previous message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-22

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From: Jordi Benach jbenach {- at -} CELLS {- dot -} ES
Date: 2008-02-22