<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>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). </div><div><br></div><div>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. </div><div><br></div><div>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? </div><div><br></div><div>Regards,</div><div><br></div><div>Michael</div><div><br></div><div><br></div><div>*****************</div><div>From Scala (3.3.20)</div><div>Total number unique : 46813</div><div>From FREERFLAG</div><div>Number of Reflections = 47044 (including non-observed NaN reflections) </div><div><br></div><div>MTZ column labels</div><div>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(-)</div><div>******************</div><div>In Phenix:</div><div><br></div><div> Xtriage output choosing "Imean"</div><div>Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:IMEAN_S13E_X2,SIGIMEAN_S13E_X2</div><div>Observation type: xray.amplitude</div><div>Type of data: double, size=46772</div><div>Type of sigmas: double, size=46772</div><div>Number of Miller indices: 46772</div><div>Anomalous flag: False</div><div><br></div><div> Xtriage output choosing "Fs"</div><div>Miller array info: /Users/garavito/ccp4_projects/sus1_S13/reflections_tmp.mtz:F_S13E_X2,SIGF_S13E_X2,DANO_S13E_X2,SIGDANO_S13E_X2</div><div>Observation type: xray.amplitude</div><div>Type of data: double, size=88486</div><div>Type of sigmas: double, size=88486</div><div>Number of Miller indices: 88486</div><div>Anomalous flag: True</div><div><br></div><div apple-content-edited="true">
<p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font face="Courier" size="3" style="font: 12.0px Courier; font-family: Courier; font-size: 12px; "><i style="font-family: Courier; font-size: 12px; font-style: italic; "><span class="Apple-style-span" style="font-family: Courier; font-size: 12px; font-style: italic; ">****************************************************************</span></i></font></p><p style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 14px; "><font face="Courier" size="3" style="font: 12.0px Courier; font-family: Courier; font-size: 12px; "><i style="font-family: Courier; font-size: 12px; font-style: italic; "><span class="Apple-style-span" style="font-family: Courier; font-size: 12px; font-style: italic; ">R. 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