Hmm... thanks for the heads-up. It's a little challenging for me to stay up-to-date with these things lately. If you want to have a go at fixing it for yourself, you can find the location of the template ISOLDE uses to write the .eff file by first going to the ChimeraX shell (Tools/General/Shell) and then entering the following:

from chimerax.isolde.output.refinement.phenix import refine_input
refine_input.__file__

The template text is defined at lines 45-117: https://github.com/tristanic/isolde/blob/b6bb66c2516aa21c2fa3210e3e717f233fe58abe/isolde/src/output/refinement/phenix/refine_input.py#L45-L117. If you edit this and restart ChimeraX, the .eff file written by "isolde write phenixRefineInput" will reflect your changes. The only only real gotcha is that the Python f-string format requires you to use "{{" and "}}" anwhere you want "{" and "}" to appear in the final output.

If you do take the plunge, please get back to me and I'll look at rolling your changes into the next release.

Best,

Tristan

On Thu, Mar 13, 2025 at 4:46 PM Shawn Rumrill via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Community,

Not strictly ChimeraX related, but probably interesting to some and I've seen some feedback for ISOLDE here...

I am using ISOLDE to rebuild a mid-resolution protein/NA model (still adjusting to using ISOLDE, but really powerful tool). I want to refine using phenix.refine, but I am running into a problem with the refine.eff file. The error from the terminal output is below. I've gathered that this is due to a change in parameter terminology from Phenix 1.20 to 1.21.

My question is, is there some way to write the refine.eff file with the required information? I would hate to have to manually edit the .eff output file each time I want to run a new refinement in Phenix.

Thanks,

Shawn

Error:

Processing files:

-------------------------------------------------------------------------------

Found phil, refine.eff

Processing PHIL parameters:

-------------------------------------------------------------------------------

Adding PHIL files:

------------------

refine.eff

Unrecognized PHIL parameters:

-----------------------------

refinement.input.pdb.file_name (file "refine.eff", line 6)

refinement.input.xray_data.file_name (file "refine.eff", line 9)

refinement.input.xray_data.labels (file "refine.eff", line 10)

refinement.input.xray_data.high_resolution (file "refine.eff", line 11)

refinement.input.xray_data.low_resolution (file "refine.eff", line 12)

refinement.input.xray_data.r_free_flags.file_name (file "refine.eff", line 14)

refinement.input.xray_data.r_free_flags.label (file "refine.eff", line 15)

refinement.input.xray_data.r_free_flags.test_flag_value (file "refine.eff", line 16)

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.

PHIL parameters in files should be fully specified (e.g. "output.overwrite"

instead of just "overwrite")

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