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Thank you everybody for your inputs. Already four suggested the QC server.
I think at this point we have enough ideas.
Once again, thanks for your attention.
Debasish
From: Kumar, Abhinav [mailto:[log in to unmask]]
Sent: Thursday, October 31, 2013 6:49 PM
To: Debasish Chattopadhyay
Cc: [log in to unmask]
Subject: Re: [ccp4bb] PDB structure validation
Try JCSG QC server:
All our structures go through this server before submitted to the PDB and we rarely get any issues back from PDB.
Thanks,
Abhinav
________________________________
Abhinav Kumar, Ph.D.
Joint Center for Structural Genomics
SSRL, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992
On Oct 31, 2013, at 9:06 AM, Debasish Chattopadhyay <[log in to unmask]> wrote:
Thanks Randy.
That would be fantastic.
From: Randy
Read [mailto:[log in to unmask]]
Sent: Thursday, October 31, 2013 11:02 AM
To: Debasish Chattopadhyay
Cc: [log in to unmask]
Subject: Re: [ccp4bb] PDB structure validation
Yes, the intention at the PDB sites is to make available a standalone validation server that will run exactly the same validation tests that have been introduced for recent depositions. My understanding is that this server is currently
being tested and will be rolled out to the community sometime in the new year once they're confident that it is stable.
The motivation is exactly as you say: to save time for both the depositors and the annotators, and to improve the quality of the deposited structures!
Best wishes,
Randy Read
On 31 Oct 2013, at 15:25, Debasish Chattopadhyay <[log in to unmask]> wrote:
I was wondering if there is a way to generate a PDB validation report before depositing the coordinates so that one can go back and make necessary corrections to the file
before deposition. It will save a lot time and perhaps would improve the quality of deposited structures.
Debasish Chattopadhyay
University of Alabama at Birmingham
CBSE-250
1025 18th Street South, Birmingham, Al-35294
USA
Ph: (205)934-0124; Fax: (205)934-0480
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk