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NMR Restraints Grid

 Data flows from the original raw data to parsed, to the databases DOCR and FRED

This README describes the content of zip files downloaded from the NMR Restraints Grid at the BMRB.

Content


Organization


File name Description
readme.html This file
index.csv Index file used for looking up mr_block_id(s) for specific entries or data types
main.css Hypertext Cascading Style Sheet used by your browser for rendering the readme. Keep this file in the same directory as the readme. Not important otherwise.
errors.txt An optional file that describes any errors that might have been encountered downloading the data from the database. It is possible that modifications to the database during download removed requested blocks. That is one example that would be documented in this file.
block_123.txt File with data on the block with mr_block_id equal to e.g. 123
block_124.tgz File with binary data of a gzipped tar file with for example XML files. A full list of possible file extensions is detailed below.
block_125.txt Etc.


Using downloaded data


The data is split up into one or more blocks each in their own file called block_XXXX.txt. In order to use the data you will need the index file: index.csv. Each row contains information specific for a data file. One of the columns in the index file lists the mrblock_id.
    

Using the index file


Most spreadsheet programs, e.g. Gnumeric and MS Excel, can read csv formatted files such as the index files. Alternatively, you might want to use a scripting language such as gawk to access subsets of the data. The meaning of the all columns is documented below.

For example, to locate the block ids with the data on a specific PDB entry,  the Unix tool gawk could be used with the PDB code on the index file. E.g., replacing XXXX by the PDB code of interest in:
gawk -F',' '{if($4=="XXXX")print $2}' index.csv > block_ids.txt
Note that the field number of the PDB code might be 3 in stead of 4 depending on whether or not any BMRB codes are listed.


List of file extensions


Alphabetically sorted by filename extension.
Filename extension Explanation
aco DYANA/DIANA for dihedral angle restraints
csv Comma Separate Values
lol DYANA/DIANA upper limits for distance restraints
mtf CNS Molecular Topology File
pdb Protein DataBank
seq DYANA/DIANA sequence
str STAR: Self-defining Text Archive and Retrieval
tbl XPLOR/CNS tables of data
tgz Gzipped tar
txt General text
upl DYANA/DIANA upper limits for distance restraints
xml EXtensible Markup Language

             

List of columns in index file


Alphabetically sorted by column label.
Column Explanation
bmrb_id BMRB accession number
format Format of the data e.g. "ambi" for ambiguous distance restraints
image Molecular image of the PDB entry
in_dress True if the structure has been recalculated in DRESS
in_recoord True if the structure has been recalculated in RECOORD
item_count Total number of distance, dihedral angle, and RDC restraints. Currently only STAR formatted files generated at BMRB are counted.
mrblock_id Numeric id in the database for this block (may change over time)
mrfile_id Numeric id in the database for the file this block is part of
other_prop Other type of information e.g. "LOWER_ONLY=true" for CYANA data
pdb_id PDB code being a numeral followed by three alphanumericals
position Position of this block in the file (the first block is numbered 0)
program Program or software format, e.g. XPLOR/CNS, STAR
stage Data flows from original, parsed, converted, to filtered, see the NMR Restraint Grid paper
subtype Subtype of the data such as "NOE" for distance restraints
type Type of the data such as "distance" for distance restraints


Note: The list of allowed data in the NMR Restraints Grid is available with the Wattos documentation.

This file was last updated on: Wed Jan 14 08:28:09 CST 2009