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/
