Given the session id, I could look at the logs.
The issue with the backend software is that it requires the exptl
category to be present as it needs to know the method to determine the
type of analysis desired. For instance, an NMR structure with multiple
models will invoke clustering compared to X-ray which might perform
structure factor analysis, etc.
On 1/6/25 1:05 AM, Oleg Sobolev wrote:
Dear Manju,
Thank you for alerting us about this issue. First, of course, the
PhenixBB link for Phenix-related questions:
https://phenix-online.org/archives/list/pheni...@phenix-online.org/
Indeed, Phenix has a tool "Get PDB validation report" as pointed out
by Nicholas, which uses OneDep API:
https://www.wwpdb.org/validation/onedep-validation-web-service-interface
to send files to RCSB. Unfortunately, it is rather hard to tell what
exactly went wrong, because the information returned is limited
to literally:
=====
rD {u'status': u'failed', u'errorflag': False, u'onedep_error_flag':
False, u'statusmessage': u'ok', u'session_history':
[[u'/valws/session', u'2025 01 06 00:44:59', u'begins'],
[u'/valws/upload', u'2025 01 06 00:45:00', u'begins'],
[u'/valws/validate_request', u'2025 01 06 00:45:00', u'begins'],
[u'/valws/session_status', u'2025 01 06 00:45:06', u'begins'],
[u'/valws/session_status', u'2025 01 06 00:45:16', u'begins']],
u'onedep_status_text': u'ok', u'session_id':
u'cf5393aa2fa368827ca54e146ec5e614fb434e5b'}
=====
for your attached file.
On the bright side, I ran a quick refinement (with generated data) on
your file and phenix.refine produced a mmCIF model file with which
"Get PDB validation report" was able to obtain the report.
Additionally, "Comprehensive validation" tool in Phenix can process
your original mmCIF file and give you many of the numbers you would
get in the PDB validation report.
Please let me know (off-list or h...@phenix-online.org or PhenixBB) if
you have more questions or need further assistance with Phenix.
Best regards,
Oleg Sobolev.
On Sun, Jan 5, 2025 at 8:57 AM Manjula Ramu <manjula....@gmail.com> wrote:
Thanks, Nicholas, Ezra and Marcin.
I’ve used both the Phenix validation tool and the PDB validation
server, following the standard protocol. I tried using CIF files
generated after refinement as well as those generated after
running the PDB extract. Unfortunately, I encountered issues in
both cases.
To verify the problem, I attempted to upload a file that
previously had no issues. However, even with this file, the Phenix
validation tool failed to process it.
I will try considering Lijun's suggestions.
Thanks and Regards,
Manju
<https://www.nimhans.kar.nic.in/>
On Sun, Jan 5, 2025 at 11:19 AM Nicholas Clark
<0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
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
<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
<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
<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/
