![](https://secure.gravatar.com/avatar/0dc227eeaba59d122656f0f4cb17645b.jpg?s=120&d=mm&r=g)
Hi Alejandro,
I had the same issues with command line batch refinement. The script below works with the new syntax. Replace PREFIX, SERIAL, MTZFILE, and MODEL.PDB with your file names. Of course, change the SG, restraint files, and tls definitions to match your system. You may also want to change the refinement strategy, as the one below is not the default. For the default files in the .eff or .def files, use None as follows:
default_model = None
phil_files = None
default_phil = None
---------------------------begin refine.com---------------------------------------------
phenix.refine \
output.prefix=PREFIX \
output.serial=SERIAL \
MTZFILE \
data_manager.miller_array.labels.name=F,SIGF \
MODEL.PDB \
/titan/tanner/elbow/FAD/elbow.FAD_ideal_pdb.004.cif \
/titan/tanner/elbow/NAD/NAD.cif \
/titan/tanner/elbow/FAD/FDA4.cif \
refinement.crystal_symmetry.space_group="P 1 21 1" \
refine.strategy=tls+individual_sites+individual_sites_real_space+individual_adp+rigid_body \
refine.adp.tls="chain A and peptide" \
refine.adp.tls="chain B and peptide" \
refine.sites.rigid_body="chain A" \
refine.sites.rigid_body="chain B" \
main.simulated_annealing=False \
main.ordered_solvent=False \
ordered_solvent.secondary_map_and_map_cc_filter.poor_cc_threshold=0.75 \
ordered_solvent.h_bond_min_mac=2.4 \
ordered_solvent.h_bond_min_sol=2.4 \
main.number_of_macro_cycles=3 \
output.write_model_cif_file=False \
output.write_geo_file=False
------------------end refine.com------------------------------------------------
Best Regards,
Jack Tanner
-----------------------
John J. Tanner
Professor of Biochemistry and Chemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: [email protected]mailto:[email protected]
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A
From: Alejandro Buschiazzo