<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Ralf,</div><div><br></div><div>No, this is no real problem as we have now solved it locally by deleting or rearranging columns in sftools. Using phenix.reflection_file_convert would work just as well. The point is that input and output formats tend to be obscured for the GUI users (which tend to be the younger users). Having a phenix page or wiki which briefly informs users of file handling and input/output data order would be helpful. Some of our efforts involve comparing CCP4 and Phenix results, which means that compatible mtz files are required. The nuts and bolts of CCP4 tends to be a little more transparent than in Phenix, but I like the data handling organization in Phenix. As the two program suites diverge in philosophy and implementation, the differences will need to be highlighted for users who want to use both. Thanks for the help.</div><div><br></div><div>Cheers,</div><div><br></div><div>Michael</div><br><div apple-content-edited="true">
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<br><div><div>On Oct 21, 2011, at 6:04 PM, Ralf Grosse-Kunstleve wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div class="gmail_quote"><div>Hi Michael,</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">I did notice that CCP4 6.2.0 outputs the mtz file with this column order:<div class="im">
<br>H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 DANO_S13E_X2 SIGDANO_S13E_X2 <br>F_S13E_X2(+) SIGF_S13E_X2(+) F_S13E_X2(-) SIGF_S13E_X2(-) ISYM_S13E_X2 <br>IMEAN_S13E_X2 SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-) <br>
SIGI_S13E_X2(-)<br></div></div></blockquote><div><br></div><div>This new <font class="Apple-style-span" face="'courier new', monospace">F,SIGF,DANO,SIGDANO</font> order explains why the four MTZ columns are combined into an anomalous array. (The phenix tools have been doing this for many years.)</div>
<div><br></div><div>Is this an actual problem for you?</div><div><br></div><div>You could use <font class="Apple-style-span" face="'courier new', monospace">phenix.reflection_file_convert --non-anomalous</font> to obtain a non-anomalous array.</div>
<div><br></div><div>In phenix.refine you can say <font class="Apple-style-span" face="'courier new', monospace">force_anomalous_flag_to_be_equal_to=False</font>.</div><div><br></div><div>Ralf</div><div><br></div></div>
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