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]
https://cafnrfaculty.missouri.edu/tannerlab/

Lab: Schlundt Annex rooms 3,6,9, 203B, 203C

Office: Schlundt Annex 203A

From: Alejandro Buschiazzo <[email protected]>
Date: Tuesday, July 30, 2024 at 12:13 PM
To: phenixbb <[email protected]>
Subject: [phenixbb] phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb

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Dear phenix users/developers


Some time ago there were several modifications on the names/specifications of important parameters/options (such as miller_array for structure factor files, etc)
Running phenix.refine by command lines (no gui) is my favorite, and I am now running into several difficulties:

1- what’s the difference between miller_array and default_miller_array; or model and default_model?
2- what’s the precise definition of phil_files and default_phil? What to change if I manually edit my .eff?
3- how should I use the new automatically created .def file for subsequent refinement cycles after I’ve manually rebuilt (I need to point to the new pdb input file: I usually screw this up, can’t seem to use the newly created .def as my starting instructions file anymore, it complains that I have problems in the right definition of the input pdb, or too many models...)
4- I often fall into a loop where by default newly created .eff files include a dry_run=true option (e.g. when I deliberately tell phenix.refine to overwrite previous .eff files)

Thanks a lot for clarifying on these issues: and sorry, for I couldn’t find obvious answers to them in the documentation (probably my fault!!)

Also, I am using phenix v 1.21.1-5286 (on a Sonoma MacOS laptop)

With best wishes
Alejandro

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