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:[email protected]] Sent: Thursday, October 31, 2013 6:49 PM To: Debasish Chattopadhyay Cc: [email protected] Subject: Re: [ccp4bb] PDB structure validation Try JCSG QC server: http://smb.slac.stanford.edu/jcsg/QC/ 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 <[email protected]<mailto:[email protected]>> wrote: Thanks Randy. That would be fantastic. From: Randy Read [mailto:[email protected]] Sent: Thursday, October 31, 2013 11:02 AM To: Debasish Chattopadhyay Cc: [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> 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 Hills Road E-mail: [email protected]<mailto:[email protected]> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
