From d2f813ccd1b4085484af53a70a18b9485a991847 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Tue, 17 Aug 2010 09:05:24 -0400 Subject: [PATCH] Update WLC/FJC fitting section of doc/tutorial.txt --- doc/tutorial.txt | 44 ++++++++++++++++++++++++++++---------------- 1 file changed, 28 insertions(+), 16 deletions(-) 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- 2.26.2