Re: [ccp4bb] Spacegroup choices, reindexing and so on

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CCP4bb <-- 2008 <-- January 2008 <-- 21 January 2008

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Subject: Spacegroup choices, reindexing and so on
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-01-21

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From: Clemens Schulze-Briese clemens {- dot -} schulze {- at -} PSI {- dot -} CH
Date: 2008-01-21

Subject: Re: Spacegroup choices, reindexing and so on
From: "Manfred S {- dot -} Weiss" msweiss {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-01-21

Dear Graeme,

here is what I would do, or what I would like to have.

If you are able to identify the Laue group of the data with
some degree of certainty, then all of the processing and
scaling should be carried out in this Laue group.

Then, by looking at systematic absences you may give probabilities
for each of the possible space groups, i.e. each of the eight
possibilities in P-orthorhombic. Typically one option will
have the highest probability and this is the one which should
be written out. In a second run, the user should be given the
choice of overriding this.

Now, for space groups such as P222_1, this should always be
reindexed to standard setting, if it turns out to be the one
with the highest probability.

Hope that helps,

Manfred.

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On Mon, 21 Jan 2008, Winter, G (Graeme) wrote:

> Hi All,
>
> A user question about the xia2 behaviour has opened a pot of worms, and
> I thought I would ask the community for opinions. If (for example) you
> are using an automated data processing or analysis tool, and the
> systematic absences suggest a spacegroup choice, what would you like to
> do:
>
> (1) nothing - just mention this in the output
> (2) assign the "base" version of this spacegroup (e.g. P41212 to
> represent that or it's enantiomorph)
> (3) create multiple copies of the reflection file with all of the
> spacegroup options
>
> As a further question, if the spacegroup looks like P 2 21 21 (say)
> would you like this to be reindexed to the standard setting?
>
> Now, I suspect that there will be a wide range of opinions on this.
>
> Following #1 will give possibly strange effects if truncate tries to
> inflate systematically absent reflections
> Following #2 will result in reflections being removed by truncate
> #3 gives lots of reflection files and lots of mess
>
> Currently I follow #2 with reindexing to the standard setting.
>
> There have been discussions in the past of being able to flag "or
> enantiomorph" in the spacegroup definition in the mtz file. This would
> be useful here, but would not really help with the reindex or no
> question...
>
> Thanks!
>
> Graeme
>
>

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CCP4bb <-- 2008 <-- January 2008 <-- 21 January 2008

Previous message:
Subject: Spacegroup choices, reindexing and so on
From: "Winter, G (Graeme)" g {- dot -} winter {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-01-21

Next message:
Subject: Swiss Light Source - Beamline Scientist Position
From: Clemens Schulze-Briese clemens {- dot -} schulze {- at -} PSI {- dot -} CH
Date: 2008-01-21