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