+ 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. + +