[phenixbb] Re: Fw: Unable to open phenix.refine

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 wrote:

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