ASTRAL RAF Sequence Maps
The Protein Data Bank now provides XML
files that include a mapping between the
records SEQRES (representing the
sequence of the molecule used in an experiment) and
(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
Starting with Astral 1.73,
RAF sequence maps are
generated from the XML files.
The RAF maps summarize the
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
click here (185 MB)
Description of Format
The RAF file contains one line per PDB chain. Each line contains two parts: the header and the
Here is an example of the header format:
101m_ 0.02 38 010301 111011 0 153
^1 ^2 ^3 ^4 ^5 ^6 ^7 ^8
A '_' for the chain ID indicates a
blank chain ID. The chain
ID is case sensitive.
Most chains currently in the
have an upper case chain ID.
version number the RAF format,
currently 0.02. See below for a description of changes in the format from 0.01 to 0.02.
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.
(last modification time of the PDB file)
set of 1-bit flags (if set: 1->mapped, 2->active,
3->checked, 4->manually edited, 5->ok, 6->one-to-one
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
first non-blank residue identifier (PDB
format, 4ch+1 for the insertion code)
last non-blank residue identifier (PDB
format, 4ch+1 for the insertion code)
- 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
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
GLU, and the protein sequence listed in
the ATOM records is
The CYS has insertion
code 'A'. There are no ATOM records
corresponding to the SEQRES records for
the ALA or the
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
which comes after the first identified residue).
is mysteriously mutated to a
in the SEQRES records, and
THR 6 is missing from the
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
Some bibliographic PDB entries
(entries with sequences but not coordinates) have been added to
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