<div dir="ltr">Hi Kristoffer,<div><br></div><div>Are you running from the command-line? The current GUI in 1.21 does not support joint refinement. We will release 1.21.1 to add support.</div><div><br></div><div>If you use the command-line, the presence of the xray and neutron scopes will switch the parser to process the parameter file for joint xn refinement. You should see a log that looks like</div><div><br></div><div><font face="monospace">Starting phenix.refine<br>on Sat Feb 24 05:50:17 2024 by bkpoon <br>===============================================================================<br> <br>Processing files: <br>-------------------------------------------------------------------------------<br> <br> Found phil, params.eff <br> <br>Processing PHIL parameters: <br>------------------------------------------------------------------------------- <br> <br> Adding PHIL files: <br> ------------------ <br> params.eff <br> <br>Switching to joint x-ray/neutron refinement mode <br>-------------------------------------------------------------------------------<br></font></div><div><br></div><div>The 1.21.1 release will probably be next week. I'm currently testing the GUI. Thanks!</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Feb 23, 2024 at 11:58 AM Tim Gruene <<a href="mailto:tim.gruene@univie.ac.at">tim.gruene@univie.ac.at</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hello Kristoffer,<br>
<br>
maybe this is related to the first paragraph at the link that you<br>
provide ("The paradigm and implementation of the joint X-ray and<br>
neutron refinement were changed in the fall of 2023, as documented<br>
here: <a href="https://pubmed.ncbi.nlm.nih.gov/37942718/" rel="noreferrer" target="_blank">https://pubmed.ncbi.nlm.nih.gov/37942718/</a>"): <br>
<br>
It is better to use the information from an X-ray dataset via<br>
geometric restraints and refine against neutron data only (cf. DOI<br>
10.1107/S1600576713027659), so that you focus on the information from<br>
the neutron data.<br>
<br>
Cheers,<br>
TIm<br>
<br>
On Fri, 23 Feb 2024 10:58:17 +0000 Kristoffer Lundgren<br>
<<a href="mailto:kristoffer.lundgren@compchem.lu.se" target="_blank">kristoffer.lundgren@compchem.lu.se</a>> wrote:<br>
<br>
> Hello phenixbb,<br>
> <br>
> When trying to do joint refinement in phenix.refine 1.21-5207 using<br>
> the suggested joint_xn.eff file found at<br>
> <a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement" rel="noreferrer" target="_blank">https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement</a><br>
> as a template I get some error messages (running phenix.refine from<br>
> the command line):<br>
> <br>
> Unrecognized PHIL parameters:<br>
> -----------------------------<br>
> xray.refinement.refine.strategy (file "joint_xn.eff", line 33)<br>
> xray.refinement.main.simulated_annealing (file "joint_xn.eff",<br>
> line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff",<br>
> line 37) xray.refinement.main.number_of_macro_cycles (file<br>
> "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file<br>
> "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing<br>
> (file "joint_xn.eff", line 48)<br>
> neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line<br>
> 49) neutron.refinement.main.number_of_macro_cycles (file<br>
> "joint_xn.eff", line 50)<br>
> <br>
> Can you please advice on how to proceed? It looks like the options<br>
> supplied are not recognized at all by phenix.refine.<br>
> <br>
> Best regards<br>
> Kristoffer<br>
> <br>
> <br>
> From: <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>> on behalf of Derek Logan<br>
> <<a href="mailto:derek.logan@biochemistry.lu.se" target="_blank">derek.logan@biochemistry.lu.se</a>> Date: Monday, 22 January 2024 at<br>
> 09:39 To: "<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>" <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
> Cc: Ulf Ryde <<a href="mailto:ulf.ryde@compchem.lu.se" target="_blank">ulf.ryde@compchem.lu.se</a>>, "<a href="http://esko.oksanen_ess.eu" rel="noreferrer" target="_blank">esko.oksanen_ess.eu</a>"<br>
> <<a href="mailto:esko.oksanen@ess.eu" target="_blank">esko.oksanen@ess.eu</a>> Subject: ***SPAM*** [phenixbb] Joint X-ray /<br>
> neutron refinement<br>
> <br>
> Hi phenixbb,<br>
> <br>
> I'm trying to understand the current status of joint X-ray/neutron<br>
> refinement in phenix.refine. The announcement of the latest release<br>
> mentions a change in the algorithm as described in the recent<br>
> publication. In the documentation:<br>
> <br>
> Structure refinement in<br>
> PHENIX<<a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement" rel="noreferrer" target="_blank">https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement</a>><br>
> <a href="http://phenix-online.org" rel="noreferrer" target="_blank">phenix-online.org</a><<a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement" rel="noreferrer" target="_blank">https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement</a>><br>
> <br>
> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<<a href="https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement" rel="noreferrer" target="_blank">https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement</a>><br>
> <br>
> <br>
> <br>
> it's described how you can run joint refinement using a parameter<br>
> file. Does this mean that it is *only* possible in this way and not<br>
> through the GUI? The GUI was very useful in the past as it<br>
> automatically opened Coot with the maps for both X-rays and neutrons,<br>
> and the refinement statistics for both were displayed in the GUI. As<br>
> far as I can see joint refinement via the GUI last worked in version<br>
> 1.19.2-4148 from 2021.<br>
> <br>
> Best regards<br>
> Derek<br>
<br>
<br>
<br>
-- <br>
--<br>
Tim Gruene<br>
Head of the Centre for X-ray Structure Analysis<br>
Faculty of Chemistry<br>
University of Vienna<br>
<br>
Phone: +43-1-4277-70202<br>
<br>
GPG Key ID = A46BEE1A<br>
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