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 importanthttps://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 mailto:[email protected]> 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]mailto:[email protected] To unsubscribe send an email to [email protected]mailto:[email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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 importanthttps://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 mailto:[email protected]> 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]mailto:[email protected] To unsubscribe send an email to [email protected]mailto:[email protected] Unsubscribe: phenixbb-leave@%(host_name)s