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=f52c98ba9cc2d3cb0d80088a41cc5fd42c3700d4;hp=015296b427afe890d4b3a1f7f3d84fcc6d417398;hb=3c323b699aa2b2003a4f61a8564dc313c7df4d66;hpb=0cc1f7b0bd3e07a048f0b7847a76ab3dd59e38de

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 015296b..f52c98b 100644
--- a/doc/manual/mussagl_manual.rst
+++ b/doc/manual/mussagl_manual.rst
@@ -791,6 +791,37 @@ Save Motif List
 See `Save Motifs to File`_ in the `Motifs`_ section.
 
 
+Viewing Multiple Analyses
+-------------------------
+
+Some times it is useful to view more than one analysis at a time. To
+do accomplish this, Mussa allows you to open a new Mussa window by
+selecting the **File > New Mussa Window** menu option.
+
+.. image:: images/new_mussa_window_menu.png
+   :alt: New Mussa Window Menu Option
+   :align: center
+
+A new Mussa window will pop up.
+
+.. figure:: images/new_mussa_window.png
+   :alt: New Mussa Window
+   :align: center
+
+   A new Mussa window on the right, in which I have loaded a second
+   experiment.
+
+Now you can create or load an existing analysis, in this new window,
+as described in the `Create/Load Analysis`_ section. 
+
+You can view as many analyses as you can fit on your screen or until
+you run out of available RAM. If you notice a rapid decrease in
+performance and hear lots of noise coming from your hard drive, you
+probably ran out of RAM and are now using virtual memory (i.e. much
+much slower). If this happens, you may need to avoid opening as many
+analyses at one time.
+
+
 Annotations / Motifs
 --------------------
 
@@ -991,6 +1022,7 @@ as shown in the screen shot below, and do one of the following:
    :alt: Copy sequence
    :align: center
 
+
 Saving to an Image
 ---------------------------------