Hi Kevin,
Thank you for the report. I would be happy to fix the issue. For this I
need to be able to reproduce it myself. Can you please share (off-list) the
inputs that you used for the refinement to produce this result? All files
will be treated confidentially.
Best regards,
Oleg Sobolev.
On Fri, Feb 7, 2025 at 12:34 PM Kevin M Jude
I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors.
Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16
ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O
ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O
TER
ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N
ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N
ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1
ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1
I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s