[phenixbb] Unusual CCP4 to Phenix data conversion result

R.M. Garavito garavito at msu.edu
Thu Oct 20 12:14:25 PDT 2011

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? 



From Scala (3.3.20)
Total number unique :   46813
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20111020/b67c5f99/attachment.htm>

More information about the phenixbb mailing list