Log a warning (rather than raising a Failure) on glob-loading a non-curve

[hooke.git] / doc / tutorial.txt

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index f4746b81d5d2ab85bf4ee770752487cae34cff12..51524b7c2cf21fceb78b96e14926b080dbc4b3c5 100644 (file)
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -42,7 +42,7 @@ to run the Hooke shell.::
 If you are running hooke from the source directory (see
 :doc:`install`), the equivalent command is::
 
-    $ python bin/hooke
+    $ python bin/hk.py
 
 You may need to give the full path for Python on Windows systems, and
 also check that the current working directory (`.`) is in your
@@ -123,7 +123,7 @@ You can list the files in the directory using ``ls`` or ``dir``
 
 Now you are ready to generate the playlist.  First, create a blank playlist::
 
-    hooke> new_playlist --name mylist
+    hooke> new_playlist --output_playlist mylist
 
 Ensure that the new playlist is active::
 
@@ -134,7 +134,8 @@ Ensure that the new playlist is active::
 The ``--`` in the ``jump_to_playlist`` command lets
 ``jump_to_playlist`` know that ``-1`` is an argument and not an
 option.  Using the bare ``--`` is a POSIX specification [#POSIX]_
-supported by the `optparse module`_.
+supported by the `optparse module`_.  You don't need to jump if
+the new playlist is your only loaded playlist.
 
 .. _optparse module:
   http://docs.python.org/library/optparse.html#callback-example-6-variable-arguments
@@ -171,7 +172,7 @@ mylist.hkp`` or ``load_playlist mylist``, Hooke will add ``.hkp`` if
 necessary.
 
 If, generating the playlist, you are including by chance a non-force
-curve file that Hooke cannot open, Hooke will print an error and
+curve file that Hooke cannot open, Hooke will log a warning and
 continue on.
 
 Navigating the playlist
@@ -190,9 +191,11 @@ You can also jump to a given curve::
 
     hooke> jump_to_curve 14
 
-will jump to the 14th curve in the playlist.  TODO: jump_to_curve
-<PATH>, where the path can be either an absolute path or a path
-relative to the directory holding the playlist file.
+will jump to the 14th curve in the playlist.
+
+.. todo:: ``jump_to_curve <PATH>``, where the path can be either an
+  absolute path or a path relative to the directory holding the
+  playlist file.
 
 Taking notes
 ------------
@@ -200,8 +203,11 @@ Taking notes
 You can take notes about the curves you are looking at.  Just type
 ``set_note`` followed by the text you want to attach to that curve.
 Hooke will save the text in your current playlist and in an external
-log file (TODO: no external file yet.  Is this important?).  The
-output will look like this::
+log file.
+
+.. todo:: No external file yet.  Is this important?
+
+The output will look like this::
 
     Notes taken at Sun Sep 17 20:42:07 2006
     /home/cyclopia/work/tris/20060620a.041 | This is a note
@@ -234,8 +240,9 @@ the filename extension, so ``export_block foo.png``, ``export_block
 foo.eps``, and ``export_block foo.txt`` will save PNG, EPS, and
 TAB-delimited text files respectively.
 
-TODO: multiple cycles?  Solution: blank lines for "breaks", add option
-to extract specific sections using Python's slice notation.
+.. todo:: Multiple cycles in exported data?  Solution: blank lines for
+  "breaks", add option to extract specific sections using Python's
+  slice notation.
 
 If you don't want the entire block, try the ``cut`` command.
 
@@ -247,28 +254,22 @@ Interacting with the plot
 Measuring distances and forces
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-You can easily zoom in the plot by dragging a rectangle on it with the
-left mouse button.  To zoom out, click the right mouse
-button. Sometimes by zooming in and out too much, you can lose the
-picture (this is probably a small bug in Matplotlib).  Just type
-``plot`` at the command line and the curve will be refreshed.
+You can move about the plot using its navigation toolbar.  See the
+`Matplotlib manual`_ for details.
+
+.. _Matplotlib manual:
+  http://matplotlib.sourceforge.net/users/navigation_toolbar.html
 
 You can measure distances and forces directly in the plot. Just issue
-the command ``distance``.  You will be asked to click two points.
-When you click a point, a blue dot should appear.  When you click the
-second point, the distances (in nanometers and piconewtons) will
-appear on the command line.  You can use ``delta`` if you prefer,
-which gives meaningful values for every kind of graph (not only force
-curves). If you want to know the coordinates of a single point, use
-``point``.
+the command ``delta``.  You will be asked to click two points.  When
+you click a point, a blue dot should appear.  When you click the
+second point, the distances will appear in the output panel.  If you
+want to know the coordinates of a single point, left click on it.
 
 Hooke automatically adjusts the position of the clicked point to the
 nearest point in the graph, so you will be always measuring distances
 and forces between points in the graph.
 
-The commands ``force`` and ``distance`` are present in the
-``generalvclamp`` plugin.
-
 Worm like chain and freely jointed chain fitting
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~