Re: [ccp4bb] Another pointless question

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Another pointless question
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-05-08

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Subject: Re: Another pointless question
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-05-08

I2 is always an alternative setting to C2, & Pointless (by default)
will choose this (since 1.2.12 I think) if it gives a smaller beta
angle than the C2 setting

I am assured that this is the IUCr approved "standard", along with
always setting primitive orthorhombic space groups with a < b < c even
if this makes eg space group 18 P 2 21 21. However, there are some
"old-fashioned" programs :-) which don't like this (arp/warp at
present for example, though I believe this will change in future), so
Pointless does offer the option SETTING SYMMETRY-BASED, also an option
in the ccp4i GUI, to choose the "reference" setting and C2

Keeping the obliquity of the cell small has some advantages: it may
make map viewing easier, and improve the accuracy of map interpolation
in programs which are a bit casual about doing this properly

Phil

On 8 May 2009, at 17:45, Ethan Merritt wrote:

> I was very surprised recently when a run of pointless chose to
> transform my data into spacegroup I2 [*]. Here are excerpts from the
> output log:
>
> %%%%%%%%%%%%
> Selecting space group I 1 2 1 as there is a single space group with
> the highest score
> Space group confidence (= Sqrt(Score * (Score - NextBestScore)))
> = 0.37
> %%%%%%%%%%%%
> The input crystal system is C-centred monoclinic
> (Cell: 291.8 98.38 148.6 90 120.3 90)
> The crystal system chosen for output is body-centred monoclinic
> (Cell: 148.6 98.38 252 90 90.33 90)
> %%%%%%%%%%%%
>
> Notice that the log file output doesn't say, for instance,
> "you might want to consider the non-standard setting I2".
> It says "there is a single space group with the highest score",
> and proceeds to convert away from the standard setting C2.
>
> I am not complaining, as in fact this solved a bit of a mystery for
> me.
> The diffraction images had originally been indexed as I222.
> Integration
> proceeded without a hitch, but the data failed miserably to scale
> acceptably.
> Running pointless immediately made clear what the problem had been.
>
> Instead I am merely curious.
> What are the criteria that pointless uses to decide such a thing?
> In this case the beta angle is _very_ near to 90. I have fed other
> C2 data sets to pointless and not seen even a mention of I2 in the
> output. Is the "score" mentioned in the log file some weighted
> function that
> says the closer beta approaches 90 after re-indexing, the more that
> re-indexing is preferred?
>
> Ethan
>
>
> [*] Not least because I had never previously encountered "I2" as the
> name of a spacegroup. Live and learn.
>
> --
> Ethan A Merritt
> Biomolecular Structure Center
> University of Washington, Seattle 98195-7742

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Another pointless question
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-05-08

Next message:
Subject: Find water in coot
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2009-05-08