Hi Alejandro,

 

I use this script only for the first round of refinement. The script generates PREFIX_001.eff early in the refinement, and then writes PREFIX_002.def file at the end of refinement. For subsequent rounds, I edit the .def file. Often, I control-C to stop to phenix.refine after PREFIX_001.eff is created, delete PREFIX_001.log to avoid overwrite error in next step, move PREFIX_001.eff to “start.eff”, edit start.eff to modify options not included in the script, and then run phenix.refine start.eff.

 

Best Regards,

 

Jack

 

 

 

From: Alejandro Buschiazzo <[email protected]>
Date: Wednesday, July 31, 2024 at 9:55 AM
To: Tanner, John <[email protected]>
Cc: phenixbb <[email protected]>
Subject: Re: [phenixbb] phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb

Dear Jack

 

Thank you very much for your message!!

 

I see that the way you worked around the problem, was to have a detailed, “fully argumented” command, for each and every cycle, actually avoiding the use of the .def file that a n-th round of refinement generates (file that is supposedly useful as initial script for the n+1-th round, just by updating the desired input pdb model).

 

In any case, it does the trick (in my case having to add several more arguments that I personally need)

 

(still don’t quite get what the default phil and model are intended for, nor the phil_files: I see you just indicate “None” for all those, which I will do)

 

Thanks again

Alejandro

 

 

 

-- 
Alejandro Buschiazzo, PhD
Associate Professor
Laboratory of Molecular & Structural Microbiology
Institut Pasteur de Montevideo
Mataojo 2020
Montevideo 11400
URUGUAY
Phone: +598 25220910 ext. 120
Fax:  +598 25224185
https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/



On 30 Jul 2024, at 2:52 PM, Tanner, John <[email protected]> wrote:

 

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

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

WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.

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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