When Astral 1.65, was built, the Protein Data Bank provided CIF files produced by the pdb2cif program. These files 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).
Because the CIF files contain known errors, the Astral RAF sequence maps were generated directly from the PDB 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.
One common reason for manual translation is the addition of post-translationally modified residues not appearing in our standard translation table. A summary of these edits to RAF lists affected PDB chains, along with residue identifiers, 3-letter codes, and the translated one-letter codes.
To download the RAF sequence maps used to generate Astral 1.65, click here (71.4 MB)
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
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:
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.
ala a val v phe f pro p met m ile i leu l asp d glu e lys k arg r ser s thr t tyr y his h cys c asn n gln q trp w gly g 2as d 3ah h 5hp e acl r aib a alm a alo t aly k arm r asa d asb d ask d asl d asq d aya a bcs c bhd d bmt t bnn a buc c bug l c5c c c6c c ccs c cea c chg a cle l cme c csd a cso c csp c css c csw c cxm m cy1 c cy3 c cyg c cym c cyq c dah f dal a dar r das d dcy c dgl e dgn q dha a dhi h dil i div v dle l dly k dnp a dpn f dpr p dsn s dsp d dth t dtr w dty y dva v efc c fla a fme m ggl e glz g gma e gsc g hac a har r hic h hip h hmr r hpq f htr w hyp p iil i iyr y kcx k llp k lly k ltr w lym k lyz k maa a men n mhs h mis s mle l mpq g msa g mse m mva v nem h nep h nle l nln l nlp l nmc g oas s ocs c omt m paq y pca e pec c phi f phl f pr3 c prr a ptr y sac s sar g sch c scs c scy c sel s sep s set s shc c shr k soc c sty y sva s tih a tpl w tpo t tpq a trg k tro w tyb y tyq y tys y tyy y agm r gl3 g smc c asx b cgu e csx c glx z