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 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/
