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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
+ <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-------------
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>
+ <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.
+ 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>
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