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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Nat,
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<div>Yes, you're right (I forgot). For autosol runs with SAD data and where remove_aniso=True, a file exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz is created with the original anomalous data is created. This is suitable for refinement.</div>
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<div>And also yes, you're right that it is much better to copy the freeR flags instead of creating a new set which could cause a lot of confusion later.</div>
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<div>All the best,</div>
<div>Tom T<br>
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<div id="divRpF204012" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Nathaniel Echols [nechols@lbl.gov]<br>
<b>Sent:</b> Monday, November 19, 2012 10:52 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] Refining Anomalous Groups<br>
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<div>On Mon, Nov 19, 2012 at 7:47 PM, Terwilliger, Thomas C <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br>
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
I'm sorry, part of the problem is that autosol exptl_fobs_phases_freeR_flags_1.mtz file does not retain the anomalous information. This is now on my list be fixed (not quickly though because I will be able to do it only when I convert a whole lot of other
things).<br>
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<div>But doesn't AutoSol write another MTZ file that is anomalous? In one of my directories I have this:</div>
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<div>exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz</div>
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<div>which definitely has F+ and F-. (I'm not certain whether this actually appears in the GUI or not - if not, sorry, that's a bug. And it may not be propagated to other programs either, which could also be misleading.)</div>
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<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
So in your case the best thing is to run phenix.refine with your original mtz file. You can create a freeR set in the GUI.</blockquote>
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<div>I wouldn't recommend creating a new test set - it is just as easy to combine the anomalous data from the original MTZ file with the R-free flags from exptl_fobs_phases_freeR_flags_1.mtz in the reflection file editor.</div>
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<div>-Nat</div>
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