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
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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