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
>
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