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")