Re: [ccp4bb] xds to mtz using pointless

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Subject: xds to mtz using pointless
From: Sabine Schneider sabine {- dot -} schneider {- at -} CUP {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-02-20

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Subject: Re: xds to mtz using pointless
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-02-20

Subject: Re: xds to mtz using pointless
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-02-20

There was a bug in Pointless for XDS reading due to my
misunderstanding of the STARTING_FRAME value, which is fixed in
version 1.2.13, available from

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.2.13.linux (eg)

Otherwise if you send me the file I'll investigate

Phil

On 20 Feb 2008, at 09:39, Sabine Schneider wrote:

> Hi everyone,
>
> I have a fine sliced dataset consisting of 720 frames (0.25dg /
> frame). I processed them with Xds and used Pointless to convert it
> to mtz for putting it in Scala. Spacegroup is P212121 and the
> resolution ~3.2. After ~200 frames the Rmerge goes up crazy and
> after 560 it is OK again. Therefore I am trying to process the the
> data in 3 wedges (1-199, 200-560, 561-720) in XDS and see how they
> scale independently and when I sort and scale them together with
> Sortmtz and Scala. When converting the .hkl file to mtz with
> pointless there is no problem with wedge 1-199. But for the other
> two wedges I am getting a Segmentation fault in Pointless (example
> see below). Or for wedge frame 200-560 I also only got an mtz file
> with batches 200 - 360. CORRECT.LP for all three wedges looks OK (at
> least to me)?
> Anyone an idea what I am missing?
>
> Thanks for you help!
>
> Sabine
>
> Matrix to transform XDS axis system to CCP4 frame:
>
0.00796, -0.006359, 0.9999

>
-0.001536, -1, -0.006347

>
1, -0.001485, -0.00797

>
> Matrix to transform XDS detector coordinates to CCP4 frame:
>
0.00796, -0.006359, 0.9999

>
-0.001536, -1, -0.006347

>
1, -0.001485, -0.00797

>
> Rotation axis in CCP4 frame: ( 0.000 0.000 1.000)
>
> Incident beam in CCP4 frame: ( 1.000 -0.000 -0.002)
>
>
> Spacegroup information obtained from library file:
> Logical Name: SYMINFO Filename: /usr/local/share/CCP4/ccp4-6.0.2/
> lib/data/syminfo.lib
>
>
> 85329 observations accepted
> Resolution range 49.140 3.016
> 6107 accepted incomplete observations with PART < 0.98, minimum 0.75
> 1214 observations flagged as MISFITS in XDS, kept here
>
> Reconstructing orientation matrix [U] from 199 observations
>
> Orientation matrix [U]:
>
0.5847, 0.1184, 0.8026

>
-0.4283, -0.7951, 0.4294

>
0.689, -0.5948, -0.4142

> Determinant = 1.000
> Segmentation fault

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CCP4bb <-- 2008 <-- February 2008 <-- 20 February 2008

Previous message:
Subject: xds to mtz using pointless
From: Sabine Schneider sabine {- dot -} schneider {- at -} CUP {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-02-20

Next message:
Subject: Re: xds to mtz using pointless
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2008-02-20