X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=doc%2Fmanual%2Fmussagl_manual.rst;fp=doc%2Fmanual%2Fmussagl_manual.rst;h=c02d631afc4420ec7d93aa67a68d6e18fa371760;hp=9d3d61ef9627ed73e325b07aa74f2a3d550e8393;hb=eaf8230970bbb87de219c83a154563f8d50afc27;hpb=16a7a04557c8ea2e5ac9a75e4b3fa6624d572893

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 9d3d61e..c02d631 100644
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -754,6 +754,43 @@ The scroll bar allows you to scroll through the sequence which is
 useful when you have zoomed in using the `zoom factor`_.
 
 
+Saving
+------
+
+Save on Close
+~~~~~~~~~~~~~
+
+FIXME: Write this.
+
+Save Analysis
+~~~~~~~~~~~~~
+
+After making changes, such as updating species names or adding/editing
+motifs, you can save these changes by selecting the **File > Save
+analysis** menu option or pressing **CTRL + S** (PC) or
+**Apple/Command Key + S** (on Mac).
+
+.. image:: images/save_analysis.png
+   :alt: Save analysis
+   :align: center
+
+Save Analysis As
+~~~~~~~~~~~~~~~~
+
+To save a copy of your analysis to a new location, select the **File >
+Save analysis as** menu option and choose a new location and name for
+your analysis.
+
+.. image:: images/save_analysis_as.png
+   :alt: Save analysis
+   :align: center
+
+Save Motif List
+~~~~~~~~~~~~~~~
+
+See `Save Motifs to File`_ in the `Motifs`_ section.
+
+
 Annotations / Motifs
 --------------------
 
@@ -792,7 +829,15 @@ To load a motif file, select **Load Motif List** item from the
 Save Motifs to File
 *******************
 
-Note: Currently not implemented
+Motifs from the `Motif Dialog`_ can be saved to file for use with
+other analyses. If you just want your motifs to be saved with your
+analysis, see the `save analysis`_ section for details.
+
+To save a motif list, select **File > Save Motifs** menu option.
+
+.. image:: images/save_motifs.png
+   :alt: Save Motifs
+   :align: center
 
 
 Motif Dialog