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. + +