Hi Pavel, Please ignore. It was a bug in a function I had defined myself to get a simple conversion of phil parameters to json format. But I will of course use an implementation for get_results_as_JSON function if that becomes available at some point. Have a nice Christmas. Rob On 19/12/2025 20:24, Pavel Afonine wrote:

Hi Rob,

I’ve started looking into this now, as I thought it was a matter of a trivial fix. When I run the command

phenix.polder 1yjp.pdb 1yjp.mtz solvent_exclusion_mask_selection="chain A and resseq 10:13" --json

with the latest version of Phenix (latest as of 3 minutes ago), I don't even get a JSON file. Instead, the output on the screen displays:

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

WARNING: The get_results_as_JSON function has not been defined for this program !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

What command did you run?

Pavel

On 12/19/25 03:29, [email protected] wrote:

...

Hi, I think there's a slight glitch in Polder which I am currently testing. The program works fine. However, the log file shows the full phil parameter for the selection string solvent_exclusion_mask_selection whereas the json file does not. As an example I have a log file:

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

   data_manager {      miller_array {        file = "../74343_262277_1_1.mtz"      }      default_miller_array = "../74343_262277_1_1.mtz"      model {        file = "../74343_262277_4_1+ligands.pdb"      }      default_model = "../74343_262277_4_1+ligands.pdb"    }    polder {      box_buffer = 5    }    solvent_exclusion_mask_selection = ( chain Y and ( ( resseq 1 and name C1 \                                       ) or ( resseq 1 and name C2 ) or ( \                                       resseq 1 and name C3 ) or ( resseq 1 and \                                       name C4 ) or ( resseq 1 and name C5 ) or \                                       ( resseq 1 and name N6 ) or ( resseq 1 \                                       and name C7 ) or ( resseq 1 and name H8 \                                       ) or ( resseq 1 and name H9 ) or ( \                                       resseq 1 and name H10 ) or ( resseq 1 \                                       and name H11 ) ))    mask_output = True    output {      overwrite = True    }

But in the polder_modified.eff.json file it reads: -------------------------------------------------------------------------------

{    "data-manager-miller-array-file": "../74343_262277_1_1.mtz",    "data-manager-default-miller-array": "../74343_262277_1_1.mtz",    "data-manager-model-file": "../74343_262277_4_1+ligands.pdb",    "data-manager-default-model": "../74343_262277_4_1+ligands.pdb",    "polder-box-buffer": 5,    "solvent-exclusion-mask-selection": "(",    "mask-output": true,    "output-overwrite": true }

Regards,

Rob _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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