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+<head>
+<title>Modeller PIR Format IO</title>
+</head>
+<body>
+ <p>
+ <strong>Modeller PIR Format IO</strong>
+ </p>
+ <p>
+ The homology modelling program, <a
+ href="http://salilab.org/modeller/"
+ >Modeller</a> 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:
+ </p>
+ <pre>>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*
+</pre>
+ <p>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.</p>
+ <p>
+ The 'Modeller Output' flag in the 'Output' tab of the Jalview <a
+ href="../features/preferences.html"
+ >Preferences dialog box</a> 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.
+ </p>
+ <p>The general format used for generating the Modeller/PIR
+ sequence description line is shown below :
+ <pre>>P1;<em>Primary_Sequence_ID</em>
+<em>sequence or structureX</em>:<em>pdb-reference if
+ available</em>:<em>start residue</em>:<em>start chain code</em>:<em>end
+ residue</em>:<em>end chain code</em>:. <em>description text</em>
+ </pre>
+ 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.
+</body>
+</html>
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