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 >>> >>> >>> >>> >>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nimhans.kar.nic.in%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cb24be23502b04099ee4708dd2da39760%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638716902966017871%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Mv5C9HdN0WpuNuFGeGRMUArYw1bpjLZPN0KRynjw0H0%3D&reserved=0> >>> >>> >>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nimhans.kar.nic.in%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cb24be23502b04099ee4708dd2da39760%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638716902966028826%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=MpYQskGYPxnNY%2F98gjPMM7t0BS3EMxNzKj8yI98ywCM%3D&reserved=0> >>>>> >>>>> ------------------------------ >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cb24be23502b04099ee4708dd2da39760%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638716902966040577%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Axfi6DKx22sLQtIKjZO0PIwmDu5yyM%2F9r5uRCVnpPcQ%3D&reserved=0> >>>>> >>>> >>>> >>>> -- >>>> Nicholas D. Clark, PhD (He/Him) >>>> University at Buffalo >>>> Department of Structural Biology >>>> Jacob's School of Medicine & Biomedical Sciences >>>> 955 Main Street >>>> Buffalo, NY 14203 >>>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cb24be23502b04099ee4708dd2da39760%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638716902966065061%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Ij8dIg6%2FSg%2BpKetZo61YFfNiiUJDDDgLoMohBFkWStI%3D&reserved=0> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cb24be23502b04099ee4708dd2da39760%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638716902966075239%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hz844tRXSKEm%2FpSDIJNN6nrZfS1f7tVS6XE2tagJHfU%3D&reserved=0> >>> >> >> >> -- >> Nicholas D. Clark, PhD (He/Him) >> University at Buffalo >> Department of Structural Biology >> Jacob's School of Medicine & Biomedical Sciences >> 955 Main Street >> Buffalo, NY 14203 >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
