Re: [ccp4bb] xds to mtz using pointless

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

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

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

Next message:
Subject: Re: crashing-out protein eluted from Nickel column
From: Vangelis Christodoulou e {- dot -} christodoulou {- at -} NKI {- dot -} NL
Date: 2008-02-20

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

That solved it! I had an older version (1.2.9). Thanks a lot!

Sabine

Phil Evans wrote:
> 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
>

CCP4bb navigation

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

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

Next message:
Subject: Re: crashing-out protein eluted from Nickel column
From: Vangelis Christodoulou e {- dot -} christodoulou {- at -} NKI {- dot -} NL
Date: 2008-02-20