[phenixbb] Re: Pdb validation report via phenix

hi On Wed, Mar 12, 2025, 11:54 PM Oleg Sobolev wrote:

Hi Tim,

Thank you for raising the awareness and sharing the details and inputs off-list. I got in touch with RCSB developers and they fixed the issue almost instantly. Please feel free to rerun your jobs and let us know of any issues!

Best regards, Oleg Sobolev.

On Fri, Mar 7, 2025 at 1:49 PM Stachowski, Tim wrote:

...

I’ve always found the phenix.get_pdb_validation tool to be super helpful to gauge where my refinements are relative to the PDB, especially since I work mainly through the command line.

But sometime around late last year, the R-free metric stopped being calculated (probably related to “EDS: FAILED”).

Is there a way to bring this part of the tool back – or does anyone have a work around they can share?

I’m running the command like:

phenix.get_pdb_validation_report final-coot-3_refine_001.reflections.cif final-coot-3_refine_001.cif

with version:

phenix-2.0rc1-5599

Thanks

Tim

--

*Tim Stachowski, PhD*

St. Jude Children’s Research Hospital

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