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: <[email protected]> on behalf of Derek Logan <[email protected]>
Date: Monday, 22 January 2024 at 09:39
To: "[email protected]" <[email protected]>
Cc: Ulf Ryde <[email protected]>, "esko.oksanen_ess.eu" <[email protected]>
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:

 

AURqZhI53yp3gAAAABJRU5ErkJggg==

 

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