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

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CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008
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Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-22 		Next 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


Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-22
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.

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

--

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*
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CCP4bb <-- 2008 <-- February 2008 <-- 22 February 2008
Previous message:
Subject: Re: XDS and overlaps -cumulative intensity distributions, E-test
From: Clemens Vonrhein vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2008-02-22 		Next 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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