[phenixbb] Joint X-ray / neutron refinement

[Kristoffer Lundgren]

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 at phenix-online.org> on behalf of Derek Logan <derek.logan at biochemistry.lu.se>
Date: Monday, 22 January 2024 at 09:39
To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Cc: Ulf Ryde <ulf.ryde at compchem.lu.se>, "esko.oksanen_ess.eu" <esko.oksanen at 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
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