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Incomplete Rfam.tar.gz mapping for Rfam>=14.0 #34

Closed filipsPL closed 4 years ago

filipsPL commented 4 years ago

It seems that the file containing mapping of rfam families to pdb codes is incomplete in rfam 14.0 and 14.1.

In 14.0 (ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.0/Rfam.tar.gz) pdb code is missing:

pdb_id  chain   pdb_start   pdb_end bit_score   evalue_score    cm_start    cm_end  hex_colour
RF00001 C   3   118 77.20   1.6e-20 1   119 0064f4
RF00001 9   1   121 77.40   1.4e-20 1   119 ebeb30
RF00001 9   1   121 77.40   1.4e-20 1   119 93c090
RF00001 B   1   121 77.40   1.4e-20 1   119 c008ae
RF00001 B   1   121 77.40   1.4e-20 1   119 8484c0

In 14.1 (ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.1/Rfam.pdb.gz) the header is missing and there is no rfam ids:

3hjw    D   1   57  48.50   1.3e-11 1   70  1fc01f
3lwo    D   1   57  48.50   1.3e-11 1   70  ff87a4
3lwp    D   1   57  48.50   1.3e-11 1   70  ebeb30
3lwq    D   1   57  48.50   1.3e-11 1   70  f29242
3lwr    D   1   57  48.50   1.3e-11 1   70  8585e6
kalvari commented 4 years ago

@filipsPL thank you for reporting this. You must have meant the Rfam.pdb.gz files, which I updated both and are now available on the ftp.

ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.0/Rfam.pdb.gz ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.1/Rfam.pdb.gz

filipsPL commented 4 years ago

Thank you, now it works perfectly! :+1: