Hi everyone,
I finally managed to write a script to do this, I will leave it here for future
reference in case someone has the same question:
# Auto-correct nomenclature errors
set_nomenclature_errors_on_read("auto-correct")
# Read in the PDB model
mol_id = read_pdb('input_model.pdb')
# Do not ask about accept/reject refinement
set_refinement_immediate_replacement(1)
# Refine zone -> refine_zone(mol_id, ch_id, res_start, res_end, altloc)
refine_zone(mol_id, 'A', 44, 64, '')
# Accept refinement
accept_regularizement()
# Write refined model
write_pdb_file(mol_id, 'refined_model.pdb')
# Exit
coot_real_exit(0)
The script can then be executed with:
coot --no-graphics --map input.map --script script.py
Best wishes,
Filomeno
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