Dear Beate,

Following Brian's response, I can add a few points.
You can submit your data in two ways via AutoDep at PDBe (EBI). Please note that AutoDep will be fairly soon replaced by a new deposition system, common to all the PDB sites.

1. Use ECI with the CCPN, create an "Entry" and deposit a resulting CCPN project. That way, you don't need to worry about the atom naming nomenclatures, formats, etc. Please see http://www.ebi.ac.uk/pdbe-apps/nmr/deposition for details on using ECI and AutoDep for NMR depositions. I'm not sure why you cannot import Zn ions into CCPN. Perhaps Rasmus can explain what you need to specify when importing the structure ensemble.

2. Submit individual files for each type of data. At this point you don't need to worry about the nomenclature in the restraints files, as BMRB will reprocess and standardise them after the data becomes public. The chemical shifts have to come as NMR-STAR V3.1 files, and atom nomenclature in the chemical shifts file and in the PDB coordinates file must match. The easiest way to get that is via ECI export menu or by using BMRB tools at http://www.bmrb.wisc.edu/software/starch/

I am aware that in both cases, residue numbering is an issue. As Brian explained, BMRB NMR-STAR format only allows numbering from residue 1, and there is an additional field, where author numbering can be put. In your communication with the PDBe annotators, once you submit, please include a request to have the residues re-numbered properly. 

Please do not hesitate to contact me with further questions.
Best wishes,
Aleks Gutmanas
NMR Project Leader
Protein Data Bank in Europe
EMBL-EBI

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Dear all

I am convinced that many things have really been improved due to the close collaboration of ccpnmr and ebi. However, I try to submit my data for two days now and I do not found out how to handle my case:
- I have an assignment file from NMRView (original residue numbering from 11-130), my NMRView allows me to export Star 2 format
- my collaborators wanted me to use numbering of the protein sequence, that means starting from 39. This I managed to change by importing everything to ccpnmr (sequence, shifts, constraints - not the coordinates, see below)
- I managed to obtain a .str file (I do not remember how) in a format in which at least the header is recognized. However, atom nomenclature is not (HB1, HB2 instead of HB2 and HB3).
- I think that I also managed to obtain a BMRB file from ccpnmr with the correct nomenclature (HB2 and HB3), however, the correlation between original sequence numbers and the chemical shift values in the table is only in the header (residue numbers in the chemical shift part are from 11-130 and not from 39-158).
- structure calculations were performed using aria.
- my structures are OK, I have two files, one with HB1/HB2 and another with HB2/HB3 - anyway, I did not perform stereospecific assignments
- I have a zinc ion in my structure, therefore, I did not manage to import my final structure ensemble into ccpnmr without loosing the zinc
Until there, I can find ways to submit in a, I think, coherent way.
BUT:
my constraint files (cns format) have the original HB1/HB2 nomenclature, in accordance with the chemical shift file from NMRView. I DID NOT FIND A WAY TO EXPORT THEM FROM CCPNMR THAT RESULTS IN HB2/HB3 NOMENCLATURE INSTEAD OF HB1/HB2 - how can I do this and make sure that my constraint involving an HB1 proton still corresponds to the identical proton from the assignment file ?

Thanks for your help

Beate

By the way, documentation from EBI concerning the PDB Deposit interface is really rudimentary ....