[phenixbb] Re: phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb

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 Date: Tuesday, July 30, 2024 at 12:13 PM To: phenixbb 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 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s