Dear Marcin, Thank you very much for this contribution to the discussion.
As you know, the entire Global Phasing team is 200% behind every word you wrote, from the first to the last! With best wishes, Gerard. -- On Sun, Jan 05, 2025 at 05:26:42PM +0100, Marcin Wojdyr wrote: > Nooo, don't do this! Use a refinement program and whatever the MX > software suite that you are using is providing to get to deposition. > You shouldn't need pdb-extract nowadays. > > > On Sun, Jan 5, 2025 at 5:07 PM Nicholas Clark > <0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > Manju, > > > > I agree with Marcin's answer. I have opened your CIF file in a text editor > > and am comparing it to a CIF I have on hand for deposition. The CIF file > > format in your file is not the same as what I have ready for deposition. > > You can try to use your PDB file and convert it to CIF for deposition using > > the PDB service for this: https://pdb-extract.wwpdb.org/ > > > > See if this corrects your issue. > > > > Best, > > > > Nick > > > > On Sun, Jan 5, 2025 at 10:52 AM Manjula Ramu <manjula....@gmail.com> wrote: > >> > >> Hi Nicholas, > >> yes, I renamed the file I tried too. > >> I still get the error. > >> > >> Thanks, > >> > >> Manju > >> > >> > >> > >> > >> > >> 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 > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> ________________________________ > >>>> > >>>> To unsubscribe from the CCP4BB list, click the following link: > >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >>> > >>> > >>> > >>> -- > >>> 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 > > > > > > > > -- > > 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/ ######################################################################## 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/