Has anyone had problems trying to open phenix.refine? I have installed Phenix 2.0.5936 several times but keep on getting the following error message when I click on phenix.refine: KeyError : 'Unrecognized input file parameter refinement.gui.migration.refinement.input.sequence.file_name (allowed: data_manager.model.file, refinement.reference_model.file, refinement.gui.migration.refinement.input.pdb.file_name, refinement.gui.migration.refinement.input.pdb.neutron_file_name, refinement.gui.migration.refinement.input.pdb.electron_file_name, refinement.den.reference_file).' Any help/advice would be much appreciated. Thanks in anticipation!
Can you send me the input parameter file off-list? In the "Job history" tab, select the job and the click on "Show details" in the row of buttons near the bottom. A new dialog shows up and there should be a path for the "Config file" relative to the job directory. That is the parameter file that the GUI tries to load. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 92R0129 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Apr 15, 2026 at 3:55 PM
Has anyone had problems trying to open phenix.refine? I have installed Phenix 2.0.5936 several times but keep on getting the following error message when I click on phenix.refine:
KeyError : 'Unrecognized input file parameter refinement.gui.migration.refinement.input.sequence.file_name (allowed: data_manager.model.file, refinement.reference_model.file, refinement.gui.migration.refinement.input.pdb.file_name, refinement.gui.migration.refinement.input.pdb.neutron_file_name, refinement.gui.migration.refinement.input.pdb.electron_file_name, refinement.den.reference_file).'
Any help/advice would be much appreciated. Thanks in anticipation! _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
Dear Billy,
Thanks so much for reaching out...really appreciate it. Sorry for the delay. I have been working at a High School Careers Fair today.
Files attached as requested.
Not sure if it is relevant but the test/tutorial files for phenix.refine work for the installation?
Many thanks for your help once more and best wishes,
Paul Tiley
________________________________
From: Billy Poon
Dear PhenixBB, I’m interested in software that estimates the pKa values of groups within ligands. I understand that the new QM-based programs in phenix have been used to estimate the pKa values of amino acids and small molecules (see Table 1 of https://pmc.ncbi.nlm.nih.gov/articles/PMC11301759/), but I’m unsure whether pKa estimation is part of the standard output of these programs. So, I guess my question is whether there is a phenix program (eLBOW, QMR?) that outputs the pKa values of titratable groups in ligands? If not, would the developers be interested in making one? Sincerely, Jack Tanner ----------------------- John J. Tanner University of Missouri Curators’ Distinguished Professor 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
Dear Billy, Good morning (hopefully when you see this?!). I just wanted to double-check that these attachments had reached you? Many thanks and best wishes, Paul Tiley ________________________________ From: Paul Tiley
Hi Paul, Can you provide more information about how to reproduce the crash? I tried to open phenix.refine from the phaser results GUI and that worked for my tutorial dataset. I can also start phenix.refine from the list of programs from the main GUI. Where is Phenix installed and what version of Windows do you have? Is the installation for only you or for all users? I'm testing on Windows 11. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 92R0129 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Mon, Apr 20, 2026 at 2:16 AM Paul Tiley
Dear Billy,
Good morning (hopefully when you see this?!).
I just wanted to double-check that these attachments had reached you?
Many thanks and best wishes,
Paul Tiley
------------------------------ *From:* Paul Tiley
*Sent:* Thursday, April 16, 2026 7:54 PM *To:* Billy Poon *Cc:* [email protected] *Subject:* Re: [phenixbb] Unable to open phenix.refine Dear Billy,
Thanks so much for reaching out...really appreciate it. Sorry for the delay. I have been working at a High School Careers Fair today.
Files attached as requested.
Not sure if it is relevant but the test/tutorial files for phenix.refine work for the installation?
Many thanks for your help once more and best wishes,
Paul Tiley ------------------------------ *From:* Billy Poon
*Sent:* Thursday, April 16, 2026 4:58 AM *To:* Paul Tiley *Cc:* [email protected] *Subject:* Re: [phenixbb] Unable to open phenix.refine You don't often get email from [email protected]. Learn why this is important https://aka.ms/LearnAboutSenderIdentification *External email:* Treat content with caution.
Can you send me the input parameter file off-list? In the "Job history" tab, select the job and the click on "Show details" in the row of buttons near the bottom. A new dialog shows up and there should be a path for the "Config file" relative to the job directory. That is the parameter file that the GUI tries to load.
-- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 92R0129 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org
On Wed, Apr 15, 2026 at 3:55 PM
wrote: Has anyone had problems trying to open phenix.refine? I have installed Phenix 2.0.5936 several times but keep on getting the following error message when I click on phenix.refine:
KeyError : 'Unrecognized input file parameter refinement.gui.migration.refinement.input.sequence.file_name (allowed: data_manager.model.file, refinement.reference_model.file, refinement.gui.migration.refinement.input.pdb.file_name, refinement.gui.migration.refinement.input.pdb.neutron_file_name, refinement.gui.migration.refinement.input.pdb.electron_file_name, refinement.den.reference_file).'
Any help/advice would be much appreciated. Thanks in anticipation! _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
participants (4)
-
Billy Poon -
p.r.tiley@pgr.reading.ac.uk -
Paul Tiley -
Tanner, John