<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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* This file is part of Jalview.
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</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:
+ 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:.:.
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.
+ 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 :