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 PHENIXhttps://phenix-online.org/documentation/reference/refinement.html#neutron-an...
phenix-online.orghttps://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
