Dear Dennis,
As Elke wrote, some parameters were changed... I'm not sure but I think
that now definitions are even more sensitive to be specified
hierarchically. I would try to this:
phenix.refine model.pdb data.mtz params.def
where params.def are:
data_manager {
fmodel {
xray_data {
r_free_flags.generate=
force_anomalous_flag_to_be_equal_to=
}
}
miller_array {
file=data.mtz
labels.name=
}
}
output.prefix=
output.serial=
output.serial_format=
Best wishes,
Martin
On 12/04/2024 16:25, Elke De Zitter wrote:
Hi,
If you indeed run phenix.refine --show-defaults=3 you will see that
many parameter names have been changed as compared to 1.20,
e.g. refinement.input.xray_data.r_free_flags.generate has been
replaced by data_manager.fmodel.xray_data.r_free_flags.generate
I haven't checked all of your parameters, but I think you will be able
to find the corresponding new names in a similar way.
I went over the unrecognized parameters for my scripts, adapted them
accordingly and it worked.
All the best,
Elke
------------------------------------------------------------------------
*From: *"Dennis Brookner" <debrook...@gmail.com>
*To: *"CCP4BB" <CCP4BB@JISCMAIL.AC.UK>
*Sent: *Friday, April 12, 2024 4:49:39 PM
*Subject: *[ccp4bb] Parameters for phenix.refine in phenix 1.21
Hey all,
I’m wondering if anyone has an example .eff script that works with
phenix.refine 1.21. My software package writes a parameters.eff file
to be run through phenix.refine, and it works fine with phenix 1.20,
but throws the error seen below with phenix 1.21 due to missing
parameters.
Based on the information here:
https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords I
have gathered that the parameters listed below are in fact not
recognized by phenix 1.21’s phenix.refine. However, I’m unable to
locate the new versions of these parameters! Does anyone know what is
going on here?
Best,
Dennis
Here’s the error message thrown by phenix.refine:
Unrecognized PHIL parameters:
-----------------------------
refinement.input.pdb.file_name (file "params.eff", line 9)
refinement.input.xray_data.file_name (file "params.eff", line 12)
refinement.input.xray_data.labels (file "params.eff", line 13)
refinement.input.xray_data.r_free_flags.generate (file "params.eff",
line 15)
refinement.input.xray_data.force_anomalous_flag_to_be_equal_to (file
"params.eff", line 17)
refinement.output.prefix (file "params.eff", line 24)
refinement.output.serial (file "params.eff", line 25)
refinement.output.serial_format (file "params.eff", line 26)
Sorry: Some PHIL parameters are not recognized by phenix.refine.
Please run this program with the --show-defaults option to see what
parameters
are available.
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