On 21/07/2022 10:49, Filomeno Sanchez Rodriguez wrote:
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
You can add the reading of the map to the script if you like using
read_ccp4_map("input.map", 0)
accept_moving_atoms() is now the preferred function name.
refine_residues(imol, residue_spec_list) is the modern interface to
refinement, where a residue spec is [chain_id, res_no, ins_code]
If you want to use coot's real space refinement without using a script,
you can use coot-mini-rsr.
Paul.
########################################################################
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/
