[phenixbb] Unusual CCP4 to Phenix data conversion result

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Thu Oct 20 12:30:49 PDT 2011


Do you still have both Phenix versions (1.7.1 and 1.7.2)?
Could you run this command with both versions and send me the outputs?

iotbx.reflection_file_reader reflections_tmp.mtz

Could you do this with mtz files from both CCP4 versions?

Alternatively, if you send me the two mtz files I'll try to find out what
causes the difference in behavior.

Ralf


On Thu, Oct 20, 2011 at 12:14 PM, R.M. Garavito <garavito at msu.edu> wrote:

> In upgrading to CCP4 6.2.0 and Phenix-1.7.2-869 (from CCP4 6.1.13 and
> Phenix-1.7.1-743, respectively) a bug has crept into reading of the MTZ
> files.  We tend to scale and merge XDS processed data with Scala in CCP4,
> then use the resulting data in CCP4 and Phenix (with great success I might
> add).
>
> However, I just noticed that in testing the upgraded CCP4 and Phenix on OSX
> 7.2 (Lion) that the MTZ file is no longer read correctly.  An example is
> below where after the output from scaling and merging of nonanomalous
> data from the CCP4i GUI gives, at the end of FREERFLAG, some 47,000
> reflections.  Putting this into xtriage or the reflection file editor in the
> Phenix GUI, one finds that the data for the F and the DANO columns are used;
> just selecting Fs alone is impossible.  The end result is a doubling of the
> reflection number and the switching of the anomalous flag on.  Processing
> with earlier versions did not do this except when actually using anomalous
> data.
>
> Why this has happened is not clear to me, but the column order in the MTZ
> file changed slightly between CCP4 6.1.13 and CCP4 6.2.0.  Any ideas, am I
> missing something, or is this a push to only refine with intensities?
>
> Regards,
>
> Michael
>
>
> *****************
> From Scala (3.3.20)
> Total number unique :   46813
> From FREERFLAG
> Number of Reflections = 47044 (including non-observed NaN reflections)
>
> MTZ column labels
> H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 DANO_S13E_X2 SIGDANO_S13E_X2
> F_S13E_X2(+) SIGF_S13E_X2(+) F_S13E_X2(-) SIGF_S13E_X2(-) ISYM_S13E_X2
> IMEAN_S13E_X2 SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-)
> SIGI_S13E_X2(-)
> ******************
> In Phenix:
>
>      Xtriage output choosing "Imean"
> Miller array info:
> /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:IMEAN_S13E_X2,SIGIMEAN_S13E_X2
> Observation type: xray.amplitude
> Type of data: double, size=46772
> Type of sigmas: double, size=46772
> Number of Miller indices: 46772
> Anomalous flag: False
>
>      Xtriage output choosing "Fs"
> Miller array info:
> /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:F_S13E_X2,SIGF_S13E_X2,DANO_S13E_X2,SIGDANO_S13E_X2
> Observation type: xray.amplitude
> Type of data: double, size=88486
> Type of sigmas: double, size=88486
> Number of Miller indices: 88486
> Anomalous flag: True
>
> ******************************************************************
>
> *R. Michael Garavito, Ph.D.*
>
> *Professor of Biochemistry & Molecular Biology*
>
> *513 Biochemistry Bldg.   *
>
> *Michigan State University      *
>
> *East Lansing, MI 48824-1319*
>
> *Office:**  **(517) 355-9724     Lab:  (517) 353-9125***
>
> *FAX:  (517) 353-9334        Email:  garavito at msu.edu*
>
> ******************************************************************
>
>
>
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