11 Hooke is a large, flexible beast, and the number of available commands
12 can be intimidating. In this section, we'll lay out the procedure for
13 analyzing a number of common experiment types. The experiment types
14 are arranged in the order that they were developed, citing the first
15 known paper in each class. If we've got a citation wrong, please
16 submit a bug report (:doc:`bugs`).
18 Velocity clamp force spectroscopy
19 =================================
21 Developed by Rief et al. [#rief1997]_, velocity clamp spectroscopy
22 measures domain unfolding forces as the tip is moved away from the
23 surface at a constant velocity.
25 .. todo:: Velocity clamp example plot.
27 Basic analysis is something like::
29 hooke> zero_surface_contact_point --block retract
30 hooke> flat_filter_peaks --block retract --min_points 1
31 hooke> zero_surface_contact_point --block retract
32 ... --ignore_after_last_peak_info_name 'flat filter peaks'
33 hooke> convert_distance_to_force --block retract
34 ... --deflection_column 'surface deflection (m)'
35 hooke> remove_cantilever_from_extension --block retract
36 hooke> flat_peaks_to_polymer_peaks --block retract
37 hooke> polymer_fit_peaks --block retract
38 hooke> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
40 The unfolding forces should be grouped by pull velocity, and the resulting
41 distributions can be fit to specific unfolding models by comparison with
42 monte-carlo simulations (see, for example, sawsim_).
44 .. [#rief1997] M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez,
46 "Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM."
48 doi: `10.1126/science.276.5315.1109 <http://dx.doi.org/10.1126/science.276.5315.1109>`_
50 .. _sawsim: http://www.physics.drexel.edu/~wking/sawsim/
52 Force clamp spectroscopy
53 ========================
55 Developed by Fernandez and Li [#fernandez2004]_, force clamp spectroscopy
56 measures the lifetime of a domain's folded state while subject to a constant
59 .. todo:: Force clamp example plot.
61 .. todo:: Force clamp example analysis.
63 .. [#fernandez2004] J.M. Fernandez, H. Li.
64 "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a
67 doi: `10.1126/science.1092497 <http://dx.doi.org/10.1126/science.1092497>`_
69 Two-color fluorescence coincidence spectroscopy
70 ===============================================
72 Developed by Clarke et al. [#clarke2007]_,...
74 .. todo:: TCCS explanation.
76 .. todo:: TCCS example plot.
78 .. todo:: TCCS example analysis.
80 .. [#clarke2007] R.W. Clarke, A. Orte, D. Klenerman.
81 "Optimized Threshold Selection for Single-Molecule Two-Color
82 Fluorescence Coincidence Spectroscopy."
84 doi: `10.1021/ac062188w <http://dx.doi.org/10.1021/ac062188w>`_