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 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/
