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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hello phenixbb,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">When trying to do joint refinement in phenix.refine 1.21-5207 using the suggested joint_xn.eff file found at
<a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement">
https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement</a> as a template I get some error messages (running phenix.refine from the command line):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> Unrecognized PHIL parameters:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> -----------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> xray.refinement.refine.strategy (file "joint_xn.eff", line 33)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> xray.refinement.main.simulated_annealing (file "joint_xn.eff", line 36)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> xray.refinement.main.ordered_solvent (file "joint_xn.eff", line 37)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> xray.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 38)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> neutron.refinement.refine.strategy (file "joint_xn.eff", line 45)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> neutron.refinement.main.simulated_annealing (file "joint_xn.eff", line 48)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line 49)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"> neutron.refinement.main.number_of_macro_cycles (file "joint_xn.eff", line 50)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Can you please advice on how to proceed? It looks like the options supplied are not recognized at all by phenix.refine.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Best regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Kristoffer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><phenixbb-bounces@phenix-online.org> on behalf of Derek Logan <derek.logan@biochemistry.lu.se><br>
<b>Date: </b>Monday, 22 January 2024 at 09:39<br>
<b>To: </b>"phenixbb@phenix-online.org" <phenixbb@phenix-online.org><br>
<b>Cc: </b>Ulf Ryde <ulf.ryde@compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen@ess.eu><br>
<b>Subject: </b>***SPAM*** [phenixbb] Joint X-ray / neutron refinement<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi phenixbb, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica;color:black"><a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement"><span style="color:#272727;text-decoration:none">Structure
refinement in PHENIX</span></a></span><span style="font-size:9.0pt;font-family:Helvetica"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Helvetica;color:black"><a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement"><span style="color:gray;text-decoration:none">phenix-online.org</span></a></span><span style="font-size:8.5pt;font-family:Helvetica"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Helvetica;color:black"><a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement"><span style="color:black;text-decoration:none"><u><span style="color:blue"><img border="0" width="36" height="36" style="width:.375in;height:.375in" id="_x0000_i1025" src="cid:image001.png@01DA664F.96830770" alt="AURqZhI53yp3gAAAABJRU5ErkJggg=="></span></u></span></a></span><span style="font-family:Helvetica"><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for
both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards<o:p></o:p></p>
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<p class="MsoNormal">Derek<o:p></o:p></p>
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