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

########################################################################

To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1

This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Reply via email to