Error trying to run cryo_fit as a phenix command

[kimdn]

Dear Doo Nam

I am trying to use cryo_fit.

Managed to install it on my computer server (rocky9), following your instructions.
I am using a .cif file as model : it is a rather huge complex, many chains (>250000 atoms).

I launch the program with the command line phenix.cryo_fit <initial_model> <target_map> )

...yet quickly, it stirs with an error "pdb file cleaning is not done, exit now”: a copy of the terminal output is pasted below.

Thank you so much for any help!
Best
Alejandro

###############################################################################################
############################### Step 0 Prepare to run cryo_fit ###############################
###############################################################################################
Current working directory: /mnt/store124/test/Alebuss/Data_test_FlaA/Test-cryofit

Assign a model file name.
Since a user provided .cif file, let's turn it into .pdb
Converting refined.cif to PDB format.
Error converting refined.cif to PDB format:
'module' object has no attribute 'write_whole_pdb_file'
Therefore, a new number_of_steps for minimization is 20000
params.cryo_fit.Options.number_of_steps_for_minimization (a real value that will be used eventually): 20000
params.cryo_fit.Options.number_of_steps_for_cryo_fit (a real value that will be used eventually): 10000
steps_list: [True, True, True, True, True, True, True, True]
cryo_fit_repository_dir: /home/alebus/test/Alebuss/My_test_apps/Phenix/phenix-1.21.1-5286/modules/cryo_fit/
User's computer's operating system: Linux

###############################################################################################
#################### Step 1: Make gro and topology file by regular gromacs ####################
###############################################################################################
Current working directory: /mnt/store124/test/Alebuss/Data_test_FlaA/Test-cryofit/steps/1_make_gro
command: python 1_before_pdb2gmx_prepare_pdb.py refined.cif 0 0 0 True
pdb file cleaning is not done, exit now

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