CIF output parsing error

[rjrich]

When attempting to open the CIF output files from Protenix using YASARA-Structure for Linux, I get the following error:

"ERROR - The (mm)CIF file could not be parsed successfully, C UNL 1 A is present in the bond section (_struct_conn), but not in the atom coordinate section (_atom_site), or the atom's alternate location indicator is missing in _struct_conn or wrong."

I am able to open the CIF file using some other programs, e.g., CCDC Hermes, PyMOL, or Schrodinger Maestro. I can then save the file in PDB format, which can then be opened in YASARA.

[cloverzizi]

Hi @rjrich, could you please provide one of your CIF files along with the input JSON file? It appears that the residue "UNL" is recorded in _struct_conn, but it's missing from the output _atom_site. If you only need to correctly process this file, you could try removing the lines related to "UNL" in _struct_conn as a workaround.

[rjrich]

Thanks for your reply. I have conferred with the developer of YASARA software, and he has revised the program to be more inclusive with respect to variations in CIF format. Now it works for opening CIF output from Protenix. Therefore, I think you could close this issue as solved. Thanks.

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On Sun, Mar 30, 2025 at 10:27 PM cloverzizi ***@***.***> wrote: Could you please provide one of your CIF files along with the input JSON file? It appears that the residue "UNL" is recorded in _struct_conn, but it's missing from the output _atom_site. If you only need to correctly process this file, you could try removing the lines related to "UNL" in _struct_conn as a workaround. — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAP6T7OPL4FN44OOX7V7OWD2XCRZRAVCNFSM6AAAAAB2AAAMMGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRUHE2DOMZWGI> . You are receiving this because you authored the thread.Message ID: ***@***.***> [image: cloverzizi]*cloverzizi* left a comment (bytedance/Protenix#97) <#97 (comment)> Could you please provide one of your CIF files along with the input JSON file? It appears that the residue "UNL" is recorded in _struct_conn, but it's missing from the output _atom_site. If you only need to correctly process this file, you could try removing the lines related to "UNL" in _struct_conn as a workaround. — Reply to this email directly, view it on GitHub <#97 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAP6T7OPL4FN44OOX7V7OWD2XCRZRAVCNFSM6AAAAAB2AAAMMGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRUHE2DOMZWGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>