Mussa Manual: Deleting a Motif

[mussa.git] / doc / manual / mussagl_manual.rst

diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst
index 015296b427afe890d4b3a1f7f3d84fcc6d417398..45df62b8074c762224e7b5d918f60637b17b40d3 100644 (file)
--- 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
 --------------------
 
@@ -908,6 +939,11 @@ To save your motifs with your analysis, see the `save analysis`_
 section. To save your motifs to a file, see the `save motifs to file`_
 section.
 
+Deleting a Motif
+^^^^^^^^^^^^^^^^
+
+To delete a motif, remove all text from the name and sequence columns
+and close the motif editor.
 
 View Mussa Alignments
 ---------------------
@@ -991,6 +1027,7 @@ as shown in the screen shot below, and do one of the following:
    :alt: Copy sequence
    :align: center
 
+
 Saving to an Image
 ---------------------------------