Given the session id, I could look at the logs.

The issue with the backend software is that it requires the exptl category to be present as it needs to know the method to determine the type of analysis desired.   For instance, an NMR structure with multiple models will invoke clustering compared to X-ray which might perform structure factor analysis, etc.




On 1/6/25 1:05 AM, Oleg Sobolev wrote:
Dear Manju,

Thank you for alerting us about this issue. First, of course, the PhenixBB link for Phenix-related questions:
https://phenix-online.org/archives/list/pheni...@phenix-online.org/

Indeed, Phenix has a tool "Get PDB validation report" as pointed out by Nicholas, which uses OneDep API: https://www.wwpdb.org/validation/onedep-validation-web-service-interface to send files to RCSB. Unfortunately, it is rather hard to tell what exactly went wrong, because the information returned is limited to literally:
=====
rD {u'status': u'failed', u'errorflag': False, u'onedep_error_flag': False, u'statusmessage': u'ok', u'session_history': [[u'/valws/session', u'2025 01 06 00:44:59', u'begins'], [u'/valws/upload', u'2025 01 06 00:45:00', u'begins'], [u'/valws/validate_request', u'2025 01 06 00:45:00', u'begins'], [u'/valws/session_status', u'2025 01 06 00:45:06', u'begins'], [u'/valws/session_status', u'2025 01 06 00:45:16', u'begins']], u'onedep_status_text': u'ok', u'session_id': u'cf5393aa2fa368827ca54e146ec5e614fb434e5b'}
=====
for your attached file.

On the bright side, I ran a quick refinement (with generated data) on your file and phenix.refine produced a mmCIF model file with which "Get PDB validation report" was able to obtain the report. Additionally, "Comprehensive validation" tool in Phenix can process your original mmCIF file and give you many of the numbers you would get in the PDB validation report.

Please let me know (off-list or h...@phenix-online.org or PhenixBB) if you have more questions or need further assistance with Phenix.

Best regards,
Oleg Sobolev.


On Sun, Jan 5, 2025 at 8:57 AM Manjula Ramu <manjula....@gmail.com> wrote:

    Thanks, Nicholas, Ezra and Marcin.

    I’ve used both the Phenix validation tool and the PDB validation
    server, following the standard protocol. I tried using CIF files
    generated after refinement as well as those generated after
    running the PDB extract. Unfortunately, I encountered issues in
    both cases.

    To verify the problem, I attempted to upload a file that
    previously had no issues. However, even with this file, the Phenix
    validation tool failed to process it.

    I will try considering Lijun's suggestions.

    Thanks and Regards,

    Manju




    <https://www.nimhans.kar.nic.in/>


    On Sun, Jan 5, 2025 at 11:19 AM Nicholas Clark
    <0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:

        Hi Ezra,

        The Phenix "Get PDB Validation Report" tool submits the data
        to the PDB validation server on your behalf:
        
https://phenix-online.org/documentation/reference/get_pdb_validation_report.html.
        From their page on the Phenix software:"Warning: This tool
        will send your model and data to RCSB servers for processing."

        They're essentially the same thing, just doesn't require you
        to physically navigate to the PDB validation web server.

        But to Ezra's point, there is a Phenix BB, as well which
        should be your "first stop" for Phenix related issues, Manju.

        Best regards,

        Nick

        On Sun, Jan 5, 2025 at 11:11 AM Ezra Peisach
        <0000d150cd71a251-dmarc-requ...@jiscmail.ac.uk> wrote:

            Are you talking about the wwPDB validation server - or
            validation report in Phenix.

            Nick mentioned server, Manjula said in Phenix.

            There are different email addresses for support from each
            service/software and you might try there.


            On 1/5/25 10:52 AM, Manjula Ramu wrote:
            Hi Nicholas,
            yes, I renamed the file I tried too.
            I still get the error.

            Thanks,

            Manju



            
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            On Sun, Jan 5, 2025 at 10:49 AM Nicholas Clark
            <ndcla...@buffalo.edu> wrote:

                Hi Maju,

                This might be a simple solution, but have you tried
                removing the ".pdb" from the ".pdb.cif" file name
                (i.e. renaming the file)? Maybe it's confusing the
                file reading package on the validation server?

                Best,

                Nick

                On Sun, Jan 5, 2025 at 10:02 AM Manjula Ramu
                <manjula....@gmail.com> wrote:

                    Dear community,

                    I encountered an issue while uploading data
                    (attached) to generate the validation report in
                    Phenix. The error message states:

                    "The PDB server reports a failure with your data.
                    Please check that your input file follows the CIF
                    specifications."

                    I faced the same error with previously uploaded
                    files as well. Since I suspect there may not be
                    any actual errors in the CIF file, I would
                    greatly appreciate your help in identifying and
                    resolving this issue.

                    Thanks and Regards,

                    Manju




                    
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