From 507c395fad41fb4e544e1df9461e2390aed584b1 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 10 Apr 2006 14:01:04 +0000
Subject: [PATCH] moved Modeller/PIR description to its own home.

---
 help/html/features/preferences.html |   16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 5f88d62..0390e25 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -94,15 +94,13 @@ the program reading the EPS file.
   will not be appended to the sequence id. </p>
 </p>
 <p><em>Use Modeller Output</em></p>
-<p>This option only applies to PIR format output. Jalview can now read and write 
-  PIR files with sequence descriptions compatible with the program <a href="http://salilab.org/modeller/">Modeller</a>. 
-  If this option is selected Jalview will write the sequence description in the 
-  following format:</p>
-<pre>&gt;P1;O80429_MAIZE
-sequence:O80429_MAIZE:1:.:140:.:.</pre>
-If a sequence description existed before the file was saved, it will be appended 
-to the new Modeller style desciption. The Jalview id/start-end option is ignored 
-if Modeller output is selected. 
+<p>This option only applies to PIR format output. Jalview
+  automatically reads PIR files with sequence descriptions compatible
+  with the program <a
+  href="http://salilab.org/modeller/">Modeller</a>.
+  If this option is selected <a href="../io/modellerpir.html">Jalview will write Modeller style PIR
+  files</a> with correct start/end numbering and PDB file association (if
+  available). The Jalview id/start-end option is ignored if Modeller output is selected.
 <p><a name="editing"><strong>Editing Preferences tab</strong></a></p>
 <p>There are currently 2 options available which can be selected / deselected. 
 </p>
-- 
1.7.10.2