ASTRAL RAF Sequence Maps

The Protein Data Bank now provides XML files that include a mapping between the PDB-format records SEQRES (representing the sequence of the molecule used in an experiment) and ATOM (representing the atoms experimentally observed). These XML files (along with the chemical dictionary) also provide information on the original identity of most residues prior to any post-translational modifications.

Starting with Astral 1.73, Astral RAF sequence maps are generated from the XML files.

The RAF maps summarize the SEQRES—ATOM relationship in a form that can be rapidly parsed in most computer languages. Errors in the mappings are corrected manually, with human interpretation of the original PDB file serving as the final arbiter in case of difficulties or discrepancies in machine translation.

Since Astral 1.75, manual edits have not been required, as XML2RAF was able to successfully generate sequences for all chains using the "parent residue" records in the PDB's chemical dictionary, as well as other records in the PDBML (XML) files. XML2RAF is free software, and is available from the Downloads > Parseable Files & Software page.

To download the RAF sequence maps used to generate Astral 2.06, click here (312.8 MB)

To download the RAF sequence maps used to generate the Astral 2.06 update on 2016-08-25, click here (326.2 MB)

Description of Format

The RAF file contains one line per PDB chain. Each line contains two parts: the header and the body.

Here is an example of the header format:

101m_ 0.02 38 010301 111011    0  153
^1    ^2   ^3 ^4     ^5     ^6   ^7   ^8

  1. PDB+chain ID. A '_' for the chain ID indicates a blank chain ID. The chain ID is case sensitive. Most chains currently in the PDB have an upper case chain ID.
  2. version number the RAF format, currently 0.02. See below for a description of changes in the format from 0.01 to 0.02.
  3. header length (i.e. the body starts in position 39, counting from 1). The header length will always be constant for every entry from a given version of RAF; however, this length may change in future versions.
  4. PDB datestamp (last modification time of the PDB file)
  5. set of 1-bit flags (if set: 1->mapped, 2->active, 3->checked, 4->manually edited, 5->ok, 6->one-to-one mapping).
    NOTE: one-to-one-mapping only means that there is a one-to-one mapping between SEQRES and ATOM sequences. It does not mean the sequences are the same, only that all the residues are seen.
  6. first non-blank residue identifier (PDB format, 4ch+1 for the insertion code)
  7. last non-blank residue identifier (PDB format, 4ch+1 for the insertion code)
  8. body starts here

The body contains one field per residue in the protein. Each field is of fixed length, 7 characters. Here is an example containing 6 residues:

   B .a   1 rr   M .i   3Acc   5 de   6A t.
---- residue identifier (B|M|E if missing, 4 ch)
    _ insertion code (' ' if missing)
     - aa one-letter code from ATOM ('.' if missing)
      - aa one letter code from SEQRES ('.' if missing)
The meaning of the characters in each field is as follows:
  • First 4 characters - residue identifier, or B|M|E if missing. These are normally derived from ATOM records, except in the case of bibliographic entries. Warning: these identifiers do not always monotonically increase. B|M|E: if a residue has no corresponding ATOM record, instead of simply having a blank field for the corresponding resid, we use B(egin), M(iddle), E(nd) for a missing residue at the beginning, in the middle, and at the end of a chain respectively. This should be useful to limit searches when scanning for a particular residue in either direction. For bibliographic entries, no ATOM records are present, so consecutive residue identifiers beginning with '1' are assigned.
  • 5th character - insertion code, or ' ' if missing.
  • 6th character - amino acid one-letter code from ATOM records, or '.' if missing.
  • 7th character - amino acid one-letter code from SEQRES records, or '.' if missing.

In the above example, the protein sequence from the SEQRES records is ALA ARG ILE CYS GLU, and the protein sequence listed in the ATOM records is ARG 1, CYS 3, ASP 5, THR 6. The CYS has insertion code 'A'. There are no ATOM records corresponding to the SEQRES records for the ALA or the ILE, so the residue identifier is replaced by a B (in the case of ALA at the beginning of the chain) or a M (in the case of ILE, which comes after the first identified residue). ASP 5 is mysteriously mutated to a GLU in the SEQRES records, and THR 6 is missing from the SEQRES records.

Changes to the format from 0.01 to 0.02

  • The PDB datestamp field now reflects the modification time of the PDB file, rather than the date the file was obtained from the PDB.
  • Some bibliographic PDB entries (entries with sequences but not coordinates) have been added to the RAF. The PDB code for these domains begins with '0'. Because residue identifiers of residues in the RAF file are normally based on the ATOM records, and the bibliographic PDB entries have no ATOM records, each residue in the RAF entries for bibliographic chains has been numbered starting at 1.

Older RAF maps for stable releases