On Fri, 7 Dec 2012, Beate Bersch wrote:
> - 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)
Even using the ECI from within CCPN, the authseqid does not get preserved
currently (maybe formatConverter itself does - Wim?) and the EBI and or
BMRB people have a habit of disregarding it even if you include it first
time!
I have found the easiest way to at least submit a file with the correct
values that they can harvest is to edit the authseqid field by hand -
nedit is good for pasting columns of numbers!
> - 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 this is a matter of the naming convetion you choose in the output
if using formatConverter. Choose IUPAC and I think these should be fixed.
> - 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).
See above - in NMRSTAR the numbering is sequential from 1, only the
authseqid field allows you to ensure the biologically relevant numbering.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
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