[phenixbb] Re: comprehensive validation (cryoem)

Hi, Thank you for your offer to help. You can download the CIF file from the following link: https://saco.csic.es/s/gqW5ei9dBwXbiz5 Please let me know if you encounter any problems accessing the file. We look forward to hearing about any progress or insights you may obtain from the analysis. Best regards, Roberto On Fri, Jun 5, 2026 at 2:26 AM Oleg Sobolev wrote:

Hi Roberto,

There might indeed be some leftover inefficiencies in the code regarding 2-character chain ids limitation.

Can you please share the model you are working on (off-list, I will treat it confidentially). I'd like to see what you are experiencing and fix it. There could be more issues than that, given that one of the SHEET senses is 9 where only -1, 0 and 1 are allowed.

Best regards, Oleg Sobolev.

On Thu, Jun 4, 2026 at 6:57 AM Roberto Marabini wrote:

...

Hi,

We are using the Phenix protocol "Comprehensive Validation (CryoEM)" (version 2.0.5936). The input structure file is provided in mmCIF format.

We have observed that the protocol fails when chain IDs contain three characters, whereas it completes successfully when chain IDs contain two characters. Based on this behavior, we suspect that the protocol may internally convert the input mmCIF file to the legacy PDB format.

Could you please confirm whether this assumption is correct?

If such a conversion is performed internally, we would also like to understand how the protocol handles structures that exceed the limitations of the PDB format, for example files containing more than 99,999 atoms or chain identifiers that are not supported by the traditional PDB specification.

When the protocol fails the following warnings are reported: Bad HELIX record, was skipped: HELIX 1 1 MET0Ah 7 HIS0Ah 14 1 8 Bad HELIX record, was skipped: HELIX 2 2 SER0Ah 25 GLU0Ah 36 1 12 ... Bad sense in SHEET record: '9'

Thank you for your help.

Best regards,

Roberto _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

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