Hi Kristoffer, 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. 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 Starting phenix.refine on Sat Feb 24 05:50:17 2024 by bkpoon =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, params.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ params.eff Switching to joint x-ray/neutron refinement mode ------------------------------------------------------------------------------- The 1.21.1 release will probably be next week. I'm currently testing the GUI. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Fri, Feb 23, 2024 at 11:58 AM Tim Gruene wrote:

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 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-an...

...

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: on behalf of Derek Logan Date: Monday, 22 January 2024 at 09:39 To: "[email protected]" Cc: Ulf Ryde , "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-an...

phenix-online.org< https://phenix-online.org/documentation/reference/refinement.html#neutron-an...

[AURqZhI53yp3gAAAABJRU5ErkJggg==]< https://phenix-online.org/documentation/reference/refinement.html#neutron-an...

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

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