From: W. Trevor King <wking@drexel.edu>
Date: Tue, 17 Aug 2010 13:05:24 +0000 (-0400)
Subject: Update WLC/FJC fitting section of doc/tutorial.txt
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=d2f813ccd1b4085484af53a70a18b9485a991847;p=hooke.git

Update WLC/FJC fitting section of doc/tutorial.txt
---

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 89a1919..80dfb53 100644
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -252,10 +252,12 @@ respectively.
 
 If you don't want the entire block, try the ``cut`` command.
 
-Interacting with the plot
--------------------------
+Analysis
+--------
 
-(no plots in command line mode...)
+The commands we have covered so far allow basic bookkeeping.  The
+point of Hooke, though, is to allow you to easily analyze force
+spectroscopy data.  We cover those analysis commands in this section.
 
 Measuring distances and forces
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -282,19 +284,29 @@ two ways around this are:
 Worm like chain and freely jointed chain fitting
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. todo:: Update WLC fitting tutorial section.
-
-You can measure by hand the parameters relative to a force peak using
-a worm-like chain fitting with the ``fit`` command.  The command by
-default automatically finds the contact point, asks for two points
-delimiting the portion to fit, and performs a two-variable fit, with
-contour length, persistence length, and their relative errors as
-output.  If desired, one can use the ``noauto`` option to manually
-click the contact point, and/or the ``pl=NUMBER`` options to impose a
-specific persistence or Kuhn length (in nanometers).  You can choose
-which model to use with ``set fit_function wlc`` or ``set fit_function
-fjc``.  See the help of the ``fit`` command from the Hooke command
-line for details.
+Polymer model fitting is a complicated beast.  To correctly fit your
+chosen model (WLC, FJC, etc.), you need to execute a multi-step
+analysis.  Hooke provides a flexible chain of curve analyisis commands
+that create new data columns (e.g. `deflection (N)`) or store
+information in a curve's `info` dictionary (e.g. `flat filter peaks`).
+You can, if necessary, adjust the names of input and output columns
+and `info` values to combine the available commands in new and useful
+ways.
+
+    hooke> zero_surface_contact_point --block retract
+    hooke> flat_filter_peaks --block retract --min_points 1
+    hooke> zero_surface_contact_point --block retract
+    ...        --ignore_after_last_peak_info_name 'flat filter peaks'
+    hooke> convert_distance_to_force --block retract
+    ...        --deflection_column 'surface deflection (m)'
+    hooke> remove_cantilever_from_extension --block retract
+    hooke> flat_peaks_to_polymer_peaks --block retract
+    hooke> polymer_fit_peaks --block retract
+    hooke> export_block --block retract --output myblock.dat
+
+See each command's `Help`_ for details.
+
+.. todo:: Discuss command stacks and polymer model fitting.
 
 Multiple curve fitting and measuring
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~