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, citating the first
15 known paper in each class. If we've got a citation wrong, please
16 submit a bug report (:doc:`bugs`).
19 Velocity clamp force spectroscopy
20 =================================
22 Developed by Rief et al. [#rief1997]_, velocity clamp spectroscopy
23 measures domain unfolding forces as the tip is moved away from the
24 surface at a constant velocity.
26 .. todo:: Velocity clamp example plot.
28 Basic analysis is something like::
30 hooke> zero_surface_contact_point --block retract
31 hooke> flat_filter_peaks --block retract --min_points 1
32 hooke> zero_surface_contact_point --block retract
33 ... --ignore_after_last_peak_info_name 'flat filter peaks'
34 hooke> convert_distance_to_force --block retract
35 ... --deflection_column 'surface deflection (m)'
36 hooke> remove_cantilever_from_extension --block retract
37 hooke> flat_peaks_to_polymer_peaks --block retract
38 hooke> polymer_fit_peaks --block retract
39 hooke> block_info --block retract --output data.yaml name 'polymer peak [0-9]*'
41 The unfolding forces should be grouped by pull velocity, and the resulting
42 distributions can be fit to specific unfolding models by comparison with
43 monte-carlo simulations (see, for example, sawsim_).
45 .. [#rief1997] M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez,
47 "Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM."
49 doi: `10.1126/science.276.5315.1109 <http://dx.doi.org/10.1126/science.276.5315.1109>`_
51 .. _sawsim: http://www.physics.drexel.edu/~wking/sawsim/
53 Force clamp spectroscopy
54 ========================
56 Developed by Fernandez and Li [#fernandez2004]_, force clamp spectroscopy
57 measures the lifetime of a domain's folded state while subject to a constant
60 .. todo:: Force clamp example plot.
62 .. todo:: Force clamp example analysis.
64 .. [#fernandez2004] J.M. Fernandez, H. Li.
65 "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a
68 doi: `10.1126/science.1092497 <http://dx.doi.org/10.1126/science.1092497>`_
70 Two-color fluorescence coincidence spectroscopy
71 ===============================================
73 Developed by Clarke et al. [#clarke2007]_,...
75 .. todo:: TCCS explanation.
77 .. todo:: TCCS example plot.
79 .. todo:: TCCS example analysis.
81 .. [#clarke2007] R.W. Clarke, A. Orte, D. Klenerman.
82 "Optimized Threshold Selection for Single-Molecule Two-Color
83 Fluorescence Coincidence Spectroscopy."
85 doi: `10.1021/ac062188w <http://dx.doi.org/10.1021/ac062188w>`_