- Modeller PIR Format IO -
-- The homology modelling program, Modeller uses a - special form of the PIR format where information about sequence - numbering and chain codes are written into the 'description' line - between the PIR protein tag and the protein alignment entry: -
->P1;Q93Z60_ARATH -sequence:Q93Z60_ARATH:1:.:118:.:. -----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ -EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSD------QSFLD-D------------- ----------------------* ->P1;PDB|1FER|_ -structureX:1FER:1:.:105:.:. -----------------------------------------------------AFVVTDNCIKCKY---TDCV -EV-CPVDCFY----EGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEK -KDPLPDAEDWDGVKGKLQHLE* --
Jalview will attempt to parse any PIR entries conforming to the - Modeller/PIR format, in order to extract the sequence start and end - numbering and (possibly) a PDB file reference. The description line - information is always stored in the sequence description string - so - no information is lost if this parsing process fails.
-- The 'Modeller Output' flag in the 'Output' tab of the Jalview Preferences dialog - box controls whether Jalview will also output MODELLER style PIR - files. In this case, any existing 'non-modeller PIR' header - information in the description string of an alignment is appended to - an automatically generated modeller description line for that - sequence. -
-The general format used for generating the Modeller/PIR - sequence description line is shown below : -
>P1;Primary_Sequence_ID -sequence or structureX:pdb-reference if - available:start residue:start chain code:end - residue:end chain code:. description text -- The first field is either sequence or structureX, depending upon the - presence of a PDB database ID for the sequence. If the protein has no - PDB reference, then the chain code is not specified, unless one - already existed when the sequence was imported into Jalview. - -