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:
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>>>
>>>
>>>
>>> --
>>> 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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