data_<string> is incorrect on the wwPDB remediated restraints files

[GoogleCodeExporter]

The data_<string> should read:

data_wwPDB_remediated_restraints_with_modified_coordinates_PDB_code_170d

'DOCR' should not be in this string.

Also, MSD needs to be changed to PDBe through out the text and the correct
full citation needs to be provided at the bottom of the header comment text.

Is this the most recent agreed upon text reviewed by John Markley? I will
check on this.

Thanks,
Eldon

Original issue reported on code.google.com by Eldon.Ul...@gmail.com on 13 Oct 2009 at 10:12

[GoogleCodeExporter]

I was reviewing the wrong files yesterday. The data_ string and header text on 
the
files that will appear in the wwPDB directory look fine, although the last 
citation
needs to be updated.

Eldon

Original comment by webmas...@bmrb.wisc.edu on 14 Oct 2009 at 3:08

[GoogleCodeExporter]

The two headers involved:

NRG:

data_DOCR_restraints_with_modified_coordinates_PDB_code_2kdr

# This NMR-STAR file contains, for PDB entry <2kdr>:
#
# - Coordinate and sequence from the PDB mmCIF file.
# - NMR restraint from the PDB MR file.
#
# In this file, the coordinates and NMR restraints share the same atom names,
# and in this way differ from the data deposited at the wwPDB. To achieve this
# aim, the NMR restraints were parsed from their original format files, and the
# coordinate and NMR restraints information was subsequently harmonized.
#
# Due to the complexity of this harmonization process, minor modifications could
# have occurred to the coordinate and/or NMR restraints information, or data
# could have been partially lost due to parsing or conversion errors. The PDB
# file therefore, remains the authoritative reference for the coordinate data,
# and the MR files remain the primary reference for the NMR restraint data.
#
# These files are generated as part of the wwPDB at the BioMagResBank (BMRB) in
# collaboration with the MSD group at the European Bioinformatics Institute
# (EBI) and the CMBI/IMM group at the Radboud University of Nijmegen.
#
# Several software packages were used to produce this file:
#
# - Wattos (Jurgen Doreleijers, formerly BMRB now at CMBI/IMM).
# - FormatConverter (Wim Vranken, MSD).
# - CCPN framework (http://www.ccpn.ac.uk/)
# - NmrStarExport (Chris Penkett, MSD).
#
# More information about this process can be found in the references below.
#
# JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL
# Markley, and EL Ulrich. BioMagResBank databases DOCR and FRED containing
# converted and filtered sets of experimental NMR restraints and coordinates
# from over 500 protein PDB structures. J.Biomol.NMR 32 (1):1-12, 2005.
#
# JF Doreleijers, W Vranken, C Penkett, J Lin, CF Schulte, G Vuister, G Vriend,
# JL Markley, EL Ulrich. BioMagResBank database `NMR Restraints Grid` with
# curated sets of experimental NMR restraints for over 4,000 protein and nucleic
# acid PDB entries. (in preperation)

linked.str

data_wwPDB_remediated_restraints_file_for_PDB_entry_2kbe

# This wwPDB archive file contains, for PDB entry 2kbe:
#
# - Coordinates and sequence information from the PDB mmCIF file
# - NMR restraints from the PDB MR file
#
# In this file, the coordinates and NMR restraints share the same atom names,
# and in this way can differ from the data deposited at the wwPDB. To
create this
# shared data, the NMR restraints were parsed from their original format files,
# and the coordinates and NMR restraints information were subsequently
harmonized.
#
# Due to the complexity of this harmonization process, minor modifications could
# have occurred to the NMR restraints information, or data could have been lost
# because of parsing or conversion errors. The PDB file remains the
# authoritative reference for the atomic coordinates and the
originally deposited
# restraints files remain the primary reference for these data.
#
# This file is generated as part of the wwPDB at the BioMagResBank (BMRB) in
# collaboration with the PDBe (formerly MSD) group at the European
# Bioinformatics Institute (EBI) and the CMBI/IMM group at the Radboud
# University of Nijmegen.
#
# Several software packages were used to produce this file:
#
# - Wattos (BMRB and CMBI/IMM).
# - FormatConverter and NMRStarExport (PDBe).
# - CCPN framework (http://www.ccpn.ac.uk/).
#
# More information about this process can be found in the references below.
# Please cite the original reference for this PDB entry and the references
# below when using data from this file.
#
# JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL
# Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED
# containing converted and filtered sets of experimental NMR restraints and
# coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12.
#
# WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL
# Markley, J Ionides, ED Laue (2005). The CCPN data model for NMR spectroscopy:
# development of a software pipeline. Proteins 59, 687-696.
#
# JF Doreleijers, W Vranken, C Penkett, J Lin, CF Schulte, G Vuister, G Vriend,
# JL Markley, EL Ulrich. BioMagResBank database `NMR Restraints Grid` with
# curated sets of experimental NMR restraints for over 4,000 protein and nucleic
# acid PDB entries. (in preparation)

Original comment by schulte....@gmail.com on 14 Oct 2009 at 3:16

[GoogleCodeExporter]

Ok, to close this issue then?

Original comment by jurge...@gmail.com on 19 Nov 2009 at 9:06

• Changed state: Verified