Do you still have both Phenix versions (1.7.1 and 1.7.2)?<div>Could you run this command with both versions and send me the outputs?</div><div><br></div><div>iotbx.reflection_file_reader reflections_tmp.mtz</div><div><br></div>
<div>Could you do this with mtz files from both CCP4 versions?</div><div><br></div><div>Alternatively, if you send me the two mtz files I'll try to find out what causes the difference in behavior.</div><div><br></div>
<div>Ralf</div><div><br><br><div class="gmail_quote">On Thu, Oct 20, 2011 at 12:14 PM, R.M. Garavito <span dir="ltr"><<a href="mailto:garavito@msu.edu">garavito@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word"><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>
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