<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Dear Thomas,<br>Thank you for the cation. And now, I always convert the mtz file to the ccp4 map (by phenix.mtz2map) before using the phenix.map_to_model, so there are not test case set in my data now. I am not sure it is a good method or not.<br>But phenix.map_to_model will always stop in
RESOLVE step:<br>######################################################################################<br>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;"> Probability that grid points are in protein region<br><br><br> 1.0 .............................................xxxxx <br> . + x . <br> . + x . <br> . + . <br> . + . <br> . +x . <br> . + . <br> p(protein) . + . <br> 0.5 . x . <br> . + . <br> . + . <br> . x+ . <br> . + . <br> . x + . <br> . xx + . <br> 0.0 .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....+........ <br></span></p><p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">Percentile of grid points</span></p>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;"> -------------------------------------------------------------------------------</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">Number of reflections in input refl_db: 0</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">Number of reflections in current array: 1</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">Discarding all extra reflections from output array</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">Number of reflections in output array with values: 0. Without: 0</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">Writing mask to memory (entire unit cell)</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">CC of prob map with current map: 1.000000 </span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">resolve exit_info:</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;"> source_file: /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos6/modules/solve_resolve/resolve/aaa_resolve_main.cpp</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;"> source_line: 1630</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;"> status: 0</span></pre>
<pre style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'courier'; color:#000000;">EndOfResolve</span></pre>#####################################################################################<br>I check the cpu, found that the CPU is still running but nothing will be outputted, and after hours waiting, this procedure will stop automatically.<br>The input is as follow:<br>phenix.map_to_model_1.12rc0-2787 RpeHgSIR_0_oasis_1.ccp4 ../resolve.seq resolution=2.8 nproc=6 segment=True is_crystal=True auto_sharpen=False use_sg_symmetry=True density_select=False truncate_at_d_min=True space_group=R3 verbose=True wang_radius=20<br><br></div><div>Are there any problems for my data or input parameters?<br>Thank you for your time!<br></div><br><br><br><div style="position:relative;zoom:1">--<br><div><font face="Helvetica, Microsoft Yahei, verdana">Wei Ding</font></div><div><span style="line-height: 23.8px;">P.O.Box 603</span></div><div>The Institute of Physics,<span style="line-height: 1.7;">Chinese Academy of Sciences</span></div><div>Beijing,<span style="line-height: 1.7;">China</span></div><div><span style="line-height: 23.8px;">100190</span></div><span style="font-family: Helvetica, 'Microsoft Yahei', verdana; ">Tel: +86-10-82649083</span><br style="font-family: Helvetica, 'Microsoft Yahei', verdana; "><span style="font-family: Helvetica, 'Microsoft Yahei', verdana; ">E-mail: dingwei</span><a href="mailto:wangli@moon.ibp.ac.cn" target="_blank" style="color: rgb(0, 51, 153); font-family: Helvetica, 'Microsoft Yahei', verdana; ">@iphy.ac.cn</a><div style="clear:both"></div></div><div id="divNeteaseMailCard"></div><br>At 2017-06-08 19:28:05, "Terwilliger, Thomas Charles" <terwilliger@lanl.gov> wrote:<br> <blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<p>Hi Wei,<br>
</p>
<p><br>
</p>
<p>I want to give a word of caution about how to use phenix.map_to_model on crystallographic data...The bottom line is you should remove the test set from your map coefficients before running phenix.map_to model on X-ray data. Here is why:<br>
</p>
<p><br>
</p>
<p>phenix.map_to_model uses real-space refinement, which is refinement against the map. If you supply map coefficients that include your test reflections, then you will be refining against data that is in your test set. This will make your Rfree invalid when
you go back and refine your model against the original crystallographic data.<br>
</p>
<p><br>
</p>
<p>To remove the test set from your map coefficients you can use:<br>
</p>
<p><br>
</p>
<p>phenix.remove_free_from_map map_coeffs=my_map_coeffs.mtz free_in=my_data_file_with_freeR_flags.mtz mtz_out=my_map_coeffs_no_free.mtz<br>
</p>
<p><br>
</p>
<p>Also note that phenix.map_to_model uses a fixed map (it does not do density modification). Consequently for most crystallographic data at moderate resolution or higher phenix.autobuild is going to do much better than phenix.map_to_model.<br>
</p>
<p><br>
</p>
<p>All the best,<br>
</p>
<p>Tom T<br>
</p>
<p><br>
</p>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> <a href="mailto:dingding830106@163.com">dingding830106@163.com</a> <<a href="mailto:dingding830106@163.com">dingding830106@163.com</a>> on behalf of <a href="mailto:dancingdream@163.com">dancingdream@163.com</a> <<a href="mailto:dancingdream@163.com">dancingdream@163.com</a>><br>
<b>Sent:</b> Tuesday, June 6, 2017 9:16 PM<br>
<b>To:</b> Terwilliger, Thomas Charles<br>
<b>Cc:</b> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re:Re: [phenixbb] phenix.map_to_model input mtz file failure</font>
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<div>Dear Thomas,<br>
I use CAD to convert the labels from FDM->FWT, PHIDM->PHFWT, then submit this job again (without
<span style="color:rgb(128,0,128)">map_coeffs_labels=...</span> ), and everything seems ok.<br>
Thank you very much for you help.<br>
Best!<br>
</div>
<br>
<br>
<div style="zoom:1">--<br>
<div><font face="Helvetica, Microsoft Yahei, verdana">Wei Ding</font></div>
<div><span style="line-height:23.8px">P.O.Box 603</span></div>
<div>The Institute of Physics,<span style="line-height:1.7">Chinese Academy of Sciences</span></div>
<div>Beijing,<span style="line-height:1.7">China</span></div>
<div><span style="line-height:23.8px">100190</span></div>
<span style="font-family:Helvetica,'Microsoft Yahei',verdana">Tel: +86-10-82649083<br>
<br style="font-family:Helvetica,'Microsoft Yahei',verdana">
</span><span style="font-family:Helvetica,'Microsoft Yahei',verdana">E-mail: dingwei</span><a href="mailto:wangli@moon.ibp.ac.cn" target="_blank" style="color:rgb(0,51,153); font-family:Helvetica,'Microsoft Yahei',verdana">@iphy.ac.cn</a>
<div style="clear:both"></div>
</div>
<div></div>
<br>
At 2017-06-07 10:32:14, "Terwilliger, Thomas Charles" <<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>> wrote:<br>
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<p>Hi Wei,<br>
</p>
<p><br>
</p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">I'm sorry for the trouble!</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)"><br>
</span></p>
<p><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)">If you supply an MTZ file that has FWT,PHFWT or similar labels, then you can skip the "labels=...." statement and it should run.</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; background-color:rgb(255,255,255)"> </span></p>
<p><br>
</p>
<p>Let me know if that does not work!<br>
All the best,<br>
</p>
<p>Tom T<br>
</p>
<p><br>
</p>
<div style="color:rgb(33,33,33)">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b>
<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>> on behalf of
<a href="mailto:dancingdream@163.com">dancingdream@163.com</a> <<a href="mailto:dancingdream@163.com">dancingdream@163.com</a>><br>
<b>Sent:</b> Tuesday, June 6, 2017 8:19 PM<br>
<b>To:</b> <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] phenix.map_to_model input mtz file failure</font>
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<div style="line-height:1.7; color:#000000; font-size:14px; font-family:Arial">
<div>Dear Phenix bb,<br>
I intend to build a initial model by phenix.map_to_model. And the command line is as follows:<br>
<span style="color:rgb(128,0,128)">phenix.map_to_model_1.12rc0-2787 map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' 'PHIDM' 'FOMDM'" seq_file=../resolve.seq is_crystal=True use_sg_symmetry=True density_select=False truncate_at_d_min=True</span><br>
</div>
and the feedback like this:<br>
<span style="color:rgb(255,0,0)">Sorry: No initial assignment made for map_coeffs. Labels used: FP,SIGFP PHIDM FOMDM.
<br>
Available labels: ['PHIB', 'FOM', 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', 'HLADM,HLBDM,HLCDM,HLDDM']<br>
NOTE: grouped labels like 'FP,SIGFP' must stay together, <br>
have commas, and have no spaces. If they come from an MTZ file,<br>
they must be in adjacent columns as well.<br>
</span>
<div><span style="color:rgb(255,0,0)">Suggested labels to use: PHIDM FOMDM<br>
</span><span style="color:rgb(0,0,0)">I try many other input format of </span>map_coeffs_labels, such as
<br>
map_coeffs_labels="FP,SIGFP PHIDM FOMDM"<br>
map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"]<br>
... ...<br>
but the result is the same. Dose anyone can tell me how to fix this problem?<br>
Thank a lot.<br>
<br>
</div>
<br>
<br>
<br>
<br>
<div style="zoom:1">--<br>
<div><font face="Helvetica, Microsoft Yahei, verdana">Wei Ding</font></div>
<div><span style="line-height:23.8px">P.O.Box 603</span></div>
<div>The Institute of Physics,<span style="line-height:1.7">Chinese Academy of Sciences</span></div>
<div>Beijing,<span style="line-height:1.7">China</span></div>
<div><span style="line-height:23.8px">100190</span></div>
<span style="font-family:Helvetica,'Microsoft Yahei',verdana">Tel: +86-10-82649083</span><br style="font-family:Helvetica,'Microsoft Yahei',verdana">
<span style="font-family:Helvetica,'Microsoft Yahei',verdana">E-mail: dingwei</span><a href="mailto:wangli@moon.ibp.ac.cn" target="_blank" style="color:rgb(0,51,153); font-family:Helvetica,'Microsoft Yahei',verdana">@iphy.ac.cn</a>
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