<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Hi,<br><br>Normally phenix.autobuild (I think phenix.refine is used in the refinement step of phenix.autobuild) will recognize the r_free_flag in the input data file (usually .mtz) whether in ccp4 convention or phenix convention. See document of autobuild, https://www.phenix-online.org/documentation/reference/autobuild.html#r-free-flags-and-test-set<br><p>"In Phenix the parameter test_flag_value sets the value of the test set
that is to be free. Normally Phenix sets up test sets with values of 0
and 1 with 1 as the free set. The CCP4 convention is values of 0 through
19 with 0 as the free set. Either of these is recognized by default in
Phenix and you do not need to do anything special. If you have any other
convention (for example values of 0 to 19 and test set is 1) then you
can specify this with test_flag_value.</p>
<p>Note that phenix.refine and AutoBuild write out PDB files that contain
the test_flag_value. AutoBuild can read this test_flag_value and use it
automatically. However if there is a conflict between this test_flag_value
and the default value based on your data file, you may have to specify which
to use."<span class="phil-name"><br></span></p><p><span class="phil-name"></span><span class="phil-help">So I think the answer is YES.</span></p><p>Best!</p><p>Lu Zuokun<br><span class="phil-help"></span></p></div><div style="position:relative;zoom:1">--<br><div style="color: rgb(51, 51, 51); font-family: 'Microsoft Yahei', verdana; font-size: 12px; line-height: 19.992000579834px;">¬���j</div><div style="color: rgb(51, 51, 51); font-family: 'Microsoft Yahei', verdana; font-size: 12px; line-height: 19.992000579834px;">�Ͽ���ѧ������վA202</div><div style="color: rgb(51, 51, 51); font-family: 'Microsoft Yahei', verdana; font-size: 12px; line-height: 19.992000579834px;"><br></div><div style="color: rgb(51, 51, 51); font-family: 'Microsoft Yahei', verdana; font-size: 12px; line-height: 19.992000579834px;">Lu Zuokun, Ph.D. Candidate</div><div style="color: rgb(51, 51, 51); font-family: 'Microsoft Yahei', verdana; font-size: 12px; line-height: 19.992000579834px;">College of Life Science, Nankai University</div><div style="clear:both"></div></div><div id="divNeteaseMailCard"></div><br>�� 2016-05-12 16:01:09��"Luca Jovine" <Luca.Jovine@ki.se> д����<br> <blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
Hi Sam,
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<div class="">I��m sure the PHENIX developers will clarify this point, but in any case you could just dump the two MTZ files to text ones:</div>
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>mtzdump hklin file1.mtz > file1.txt</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>nref -1</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>end</div>
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>mtzdump hklin file2.mtz > file2.txt</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>nref -1</div>
<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>end</div>
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<div class="">and compare whether the same reflections are flagged in both.</div>
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<div class="">HTH,</div>
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<div class="">Luca</div>
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<div class="">On 12 May 2016, at 04:59, Sam Tang <<a href="mailto:samtys0910@gmail.com" class="">samtys0910@GMAIL.COM</a>> wrote:</div>
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<div dir="ltr" class="">Dear all
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<div class="">May I enquire a simple question about AutoBuild - I input an experimental data (ccp4 mtz from Aimless) and a model from Phaser-MR to AutoBuild hoping that some mis-fit flexible regions could be re-build. May I know if the output mtz
<i class="">overall_best_refine_data.mtz</i> contains the same FreeR flags as in the input, or would AutoBuild generate a new set of FreeR? Or in other words, are the R values directly comparable if I refine against the input experimental data mtz or the overall_best_refine_data.mtz?</div>
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<div class="">Thanks!</div>
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<div class="">Cheers<br class="">
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<div style="font-size:12.7272720336914px" class=""><font class="">Sam Tang</font></div>
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<div style="font-size:12.7272720336914px" class=""><font class="">Biochemistry Programme, School of Life Sciences, CUHK</font></div>
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