<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Nat and Ralf,<br><br>I did notice that CCP4 6.2.0 outputs the mtz file with this column order:<br><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><br>But CCP4 6.1.13 outputs the mtz file with a slightly different column order:<br><br>H K L FreeR_flag F_S13E_X2 SIGF_S13E_X2 F_S13E_X2(+) SIGF_S13E_X2(+) <br>F_S13E_X2(-) SIGF_S13E_X2(-) DANO_S13E_X2 SIGDANO_S13E_X2 IMEAN_S13E_X2 <br>SIGIMEAN_S13E_X2 I_S13E_X2(+) SIGI_S13E_X2(+) I_S13E_X2(-) SIGI_S13E_X2(-)<br><br>Note that DANO_S13E_X2 and SIGDANO_S13E_X2 have shifted position and ISYM_S13E_X2 in now included.<br><br><br>Thanks for the quick response,<br><br>Michael<br><div apple-content-edited="true">
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<br><div><div>On Oct 20, 2011, at 3:30 PM, Nathaniel Echols wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On Thu, Oct 20, 2011 at 12:14 PM, R.M. Garavito <<a href="mailto:garavito@msu.edu">garavito@msu.edu</a>> wrote:<br><blockquote type="cite">However, I just noticed that in testing the upgraded CCP4 and Phenix on OSX<br></blockquote><blockquote type="cite">7.2 (Lion) that the MTZ file is no longer read correctly. An example is<br></blockquote><blockquote type="cite">below where after the output from scaling and merging of nonanomalous<br></blockquote><blockquote type="cite">data from the CCP4i GUI gives, at the end of FREERFLAG, some 47,000<br></blockquote><blockquote type="cite">reflections. Putting this into xtriage or the reflection file editor in the<br></blockquote><blockquote type="cite">Phenix GUI, one finds that the data for the F and the DANO columns are used;<br></blockquote><blockquote type="cite">just selecting Fs alone is impossible. The end result is a doubling of the<br></blockquote><blockquote type="cite">reflection number and the switching of the anomalous flag on. Processing<br></blockquote><blockquote type="cite">with earlier versions did not do this except when actually using anomalous<br></blockquote><blockquote type="cite">data.<br></blockquote><blockquote type="cite">Why this has happened is not clear to me, but the column order in the MTZ<br></blockquote><blockquote type="cite">file changed slightly between CCP4 6.1.13 and CCP4 6.2.0. Any ideas, am I<br></blockquote><blockquote type="cite">missing something, or is this a push to only refine with intensities?<br></blockquote><br>It's actually more an inherent problem with representing data as<br>merged amplitudes and anomalous differences (and how we handle them) -<br>PHENIX does not use these data as such, and instead converts them into<br>what Ralf calls "reconstructed" amplitudes, i.e. F(+) SIGF(+) F(-)<br>SIGF(-). There is potential for loss of precision in this conversion,<br>which is why we recommend against it (the Phaser-EP GUI will actually<br>complain if you try to run it with those data). The reason this<br>changed is probably F SIGF being adjacent to DANO SIGDANO in the MTZ<br>file - if they were previously separated by other columns, they would<br>not be automatically combined into a single data array.<br><br>I'm not sure if this matters for Xtriage; it will still perform the<br>analysis of anomalous signal based on the reconstructed Friedel pairs,<br>but I don't know of use of separate F+/F- will affect the other<br>analyses. It definitely makes a difference for the reflection file<br>editor and any other program which outputs these data, because they<br>will always end up as F(+) SIGF(+) F(-) SIGF(-). Unfortunately I<br>didn't take into account that the reflection file editor was doing<br>this until a few days ago, so in version 1.7.2 it will probably still<br>label the columns F SIGF DANO SIGDANO (or the equivalent) by default.<br>I think the latest nightly build should fix this bug (and several<br>others).<br><br>This is probably not an ideal situation - it might make more sense to<br>simply ignore DANO SIGDANO, just to avoid confusion, but I'm worried<br>that users will complain about PHENIX not accepting their anomalous<br>data.<br><br>-Nat<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br></body></html>