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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