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 ++ 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------------- @@ -20,26 +45,30 @@ structureX:1FER:1:.:105:.:. 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 ++ 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.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. + residue:end chain code:. description text +