Hello Kristoffer,

maybe this is related to the first paragraph at the link that you
provide ("The paradigm and implementation of the joint X-ray and
neutron refinement were changed in the fall of 2023, as documented
here: https://pubmed.ncbi.nlm.nih.gov/37942718/"):

It is better  to use the information from an X-ray dataset via
geometric restraints and refine against neutron data only (cf. DOI
10.1107/S1600576713027659), so that you focus on the information from
the neutron data.

Cheers,
TIm

On Fri, 23 Feb 2024 10:58:17 +0000 Kristoffer Lundgren
<kristoffer.lundgren@compchem.lu.se> wrote:

> Hello phenixbb,
>
> When trying to do joint refinement in phenix.refine 1.21-5207 using
> the suggested joint_xn.eff file found at
> https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement
> as a template I get some error messages (running phenix.refine from
> the command line):
>
>   Unrecognized PHIL parameters:
>   -----------------------------
>     xray.refinement.refine.strategy (file "joint_xn.eff", line 33)
>     xray.refinement.main.simulated_annealing (file "joint_xn.eff",
> line 36) xray.refinement.main.ordered_solvent (file "joint_xn.eff",
> line 37) xray.refinement.main.number_of_macro_cycles (file
> "joint_xn.eff", line 38) neutron.refinement.refine.strategy (file
> "joint_xn.eff", line 45) neutron.refinement.main.simulated_annealing
> (file "joint_xn.eff", line 48)
> neutron.refinement.main.ordered_solvent (file "joint_xn.eff", line
> 49) neutron.refinement.main.number_of_macro_cycles (file
> "joint_xn.eff", line 50)
>
> Can you please advice on how to proceed? It looks like the options
> supplied are not recognized at all by phenix.refine.
>
> Best regards
> Kristoffer
>
>
> From: <phenixbb-bounces@phenix-online.org> on behalf of Derek Logan
> <derek.logan@biochemistry.lu.se> Date: Monday, 22 January 2024 at
> 09:39 To: "phenixbb@phenix-online.org" <phenixbb@phenix-online.org>
> Cc: Ulf Ryde <ulf.ryde@compchem.lu.se>, "esko.oksanen_ess.eu"
> <esko.oksanen@ess.eu> Subject: ***SPAM*** [phenixbb] Joint X-ray /
> neutron refinement
>
> Hi phenixbb,
>
> 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:
>
> Structure refinement in
> PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement>
> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement>
>
> [AURqZhI53yp3gAAAABJRU5ErkJggg==]<https://phenix-online.org/documentation/reference/refinement.html#neutron-and-joint-x-ray-and-neutron-refinement>
>
>
>
> 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.
>
> Best regards
> Derek



--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A
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