moved Modeller/PIR description to its own home.

diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 5f88d62..0390e25 100755 (executable)
--- 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>\r
 </p>\r
 <p><em>Use Modeller Output</em></p>\r
-<p>This option only applies to PIR format output. Jalview can now read and write \r
-  PIR files with sequence descriptions compatible with the program <a href="http://salilab.org/modeller/">Modeller</a>. \r
-  If this option is selected Jalview will write the sequence description in the \r
-  following format:</p>\r
-<pre>&gt;P1;O80429_MAIZE\r
-sequence:O80429_MAIZE:1:.:140:.:.</pre>\r
-If a sequence description existed before the file was saved, it will be appended \r
-to the new Modeller style desciption. The Jalview id/start-end option is ignored \r
-if Modeller output is selected. \r
+<p>This option only applies to PIR format output. Jalview\r
+  automatically reads PIR files with sequence descriptions compatible\r
+  with the program <a\r
+  href="http://salilab.org/modeller/">Modeller</a>.\r
+  If this option is selected <a href="../io/modellerpir.html">Jalview will write Modeller style PIR\r
+  files</a> with correct start/end numbering and PDB file association (if\r
+  available). The Jalview id/start-end option is ignored if Modeller output is selected.\r
 <p><a name="editing"><strong>Editing Preferences tab</strong></a></p>\r
 <p>There are currently 2 options available which can be selected / deselected. \r
 </p>\r