Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] xds to mtz using pointless
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 20 February 2008
Previous message:
Subject: Re: xds to mtz using pointless
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-02-20 		Next message:
Subject: Re: xds to mtz using pointless
From: Sabine Schneider sabine {- dot -} schneider {- at -} CUP {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-02-20


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

versions of pointless before 1.2.13 have a problem with XDS_ASCII.HKL.
Phil fixed this in 1.2.13, which can be obtained from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/

Why don't you use XDSCONV to go to MTZ format? (and XSCALE for merging)

best,

Kay

Sabine Schneider schrieb:
> 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


--
Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 20 February 2008
Previous message:
Subject: Re: xds to mtz using pointless
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-02-20 		Next message:
Subject: Re: xds to mtz using pointless
From: Sabine Schneider sabine {- dot -} schneider {- at -} CUP {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-02-20


ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd