From: W. Trevor King <wking@tremily.us>
Date: Mon, 17 Sep 2012 18:04:39 +0000 (-0400)
Subject: posts:comparing_velocity_clamp_experiments: add expected unfolding force line.
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=195ea1793a569ececdef1a41bc17c5f925b6f832;p=blog.git

posts:comparing_velocity_clamp_experiments: add expected unfolding force line.

For comparing crunched results against previously published numbers.
---

diff --git a/posts/Comparing_velocity_clamp_experiments/crunch.py b/posts/Comparing_velocity_clamp_experiments/crunch.py
index 99fc50a..5b261c8 100755
--- a/posts/Comparing_velocity_clamp_experiments/crunch.py
+++ b/posts/Comparing_velocity_clamp_experiments/crunch.py
@@ -98,6 +98,8 @@ pull_parameters = {
     #'contour_space_parameters': None,  # use defaults
     'contour_space_parameters': {'b': _b, 'gamma': _gamma},
     'contour_space_lines': _numpy.arange(75e-9, 350e-9, 29e-9),
+    # Carrion-Vazquez, 1999, doi: 10.1073/pnas.96.7.3694
+    'expected_unfolding_force': 200e-12,
     }
 
 ## readers for your data
@@ -594,7 +596,7 @@ class Pull (Experiment):
             'vibration_temperature', 'drift_slope', 'alpha_f_offset',
             'smooth_steps', 'start_sawteeth', 'stop_sawteeth',
             'contour_space_model', 'contour_space_parameters',
-            'contour_space_lines']
+            'contour_space_lines', 'expected_unfolding_force']
         kwargs['output_parameters'] = [
             'pull_alpha_d', 'pull_velocity', 'pull_temperature']
         kwargs['output_parameter_units'] = {
@@ -653,7 +655,8 @@ class Pull (Experiment):
               xlabel='z piezo (m)', ylabel='deflection (N)',
               bounds=None, log=None, slider=None,
               contour_space_model=None, contour_space_parameters=None,
-              contour_space_lines=None, **kwargs):
+              contour_space_lines=None, expected_unfolding_force=None,
+              **kwargs):
         """Generate pull-plots with three possible abscissa.
 
         The contour-space plots are following Puchner et al., 2008.
@@ -709,6 +712,8 @@ class Pull (Experiment):
         if xlabel == 'contour-space (m)' and contour_space_lines is not None:
             for zi in contour_space_lines:
                 axes.axvline(zi, color='g')
+        if ylabel == 'deflection (N)' and expected_unfolding_force is not None:
+            axes.axhline(expected_unfolding_force, color='g')
         if bounds:
             axes.axis(bounds)
         axes.set_title('velocity clamp unfolding')
diff --git a/posts/Comparing_velocity_clamp_experiments/pull-piezo.png b/posts/Comparing_velocity_clamp_experiments/pull-piezo.png
index aa0af78..eccd7fb 100644
Binary files a/posts/Comparing_velocity_clamp_experiments/pull-piezo.png and b/posts/Comparing_velocity_clamp_experiments/pull-piezo.png differ
diff --git a/posts/Comparing_velocity_clamp_experiments/pull-protein.png b/posts/Comparing_velocity_clamp_experiments/pull-protein.png
index af0cf52..e2b8ccc 100644
Binary files a/posts/Comparing_velocity_clamp_experiments/pull-protein.png and b/posts/Comparing_velocity_clamp_experiments/pull-protein.png differ