****************** Analysis templates ****************** .. toctree:: :maxdepth: 2 Overview ======== Hooke is a large, flexible beast, and the number of available commands can be intimidating. In this section, we'll lay out the procedure for analyzing a number of common experiment types. The experiment types are arranged in the order that they were developed, citing the first known paper in each class. If we've got a citation wrong, please submit a bug report (:doc:`bugs`). Velocity clamp force spectroscopy ================================= Developed by Rief et al. [#rief1997]_, velocity clamp spectroscopy measures domain unfolding forces as the tip is moved away from the surface at a constant velocity. .. todo:: Velocity clamp example plot. Basic analysis is something like:: 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> block_info --block retract --output data.yaml name 'polymer peak [0-9]*' The unfolding forces should be grouped by pull velocity, and the resulting distributions can be fit to specific unfolding models by comparison with monte-carlo simulations (see, for example, sawsim_). .. [#rief1997] M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez, H.E. Gaub. "Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM." Science, 1997. doi: `10.1126/science.276.5315.1109 `_ .. _sawsim: http://www.physics.drexel.edu/~wking/sawsim/ Force clamp spectroscopy ======================== Developed by Fernandez and Li [#fernandez2004]_, force clamp spectroscopy measures the lifetime of a domain's folded state while subject to a constant tension. .. todo:: Force clamp example plot. .. todo:: Force clamp example analysis. .. [#fernandez2004] J.M. Fernandez, H. Li. "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein." Science, 2004. doi: `10.1126/science.1092497 `_ Two-color fluorescence coincidence spectroscopy =============================================== Developed by Clarke et al. [#clarke2007]_,... .. todo:: TCCS explanation. .. todo:: TCCS example plot. .. todo:: TCCS example analysis. .. [#clarke2007] R.W. Clarke, A. Orte, D. Klenerman. "Optimized Threshold Selection for Single-Molecule Two-Color Fluorescence Coincidence Spectroscopy." Anal. Chem., 2007. doi: `10.1021/ac062188w `_