From 00d1d522e6c7a110d273269993e2c30cc18be3e7 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Sun, 28 Apr 2013 15:59:26 -0400 Subject: [PATCH] Update to TeXLive 2011 needs protected caption subrefs To avoid: ! Argument of \@caption has an extra }. fragile \subref{} calls in \caption{} arguments need to be \protect-ed. For details, see: http://tex.stackexchange.com/questions/31817/texlive-2011-and-subfig where egreg points out that the change probably happened in the bump to caption 3.2. --- src/apparatus/afm.tex | 12 +++++------ src/apparatus/procedure.tex | 9 ++++---- src/introduction/main.tex | 23 ++++++++++---------- src/sawsim/discussion.tex | 35 +++++++++++++++--------------- src/sawsim/methods.tex | 43 +++++++++++++++++++------------------ 5 files changed, 63 insertions(+), 59 deletions(-) diff --git a/src/apparatus/afm.tex b/src/apparatus/afm.tex index 57da522..f026d5c 100644 --- a/src/apparatus/afm.tex +++ b/src/apparatus/afm.tex @@ -31,12 +31,12 @@ vertical (\cref{fig:piezo-schematic}). \hspace{.25in}% \subfloat[][]{\label{fig:piezo-schematic} \asyinclude{figures/schematic/piezo}} - \caption{\subref{fig:afm-schematic} Operating principle for an - Atomic Force Microscope\index{AFM}. A sharp tip integrated at - the end of a cantilever interacts with the sample. Cantilever - bending is measured by a laser reflected off the cantilever and - incident on a position sensitive photodetector. - \subref{fig:piezo-schematic} Schematic of a tubular + \caption{\protect\subref{fig:afm-schematic} Operating principle + for an Atomic Force Microscope\index{AFM}. A sharp tip + integrated at the end of a cantilever interacts with the sample. + Cantilever bending is measured by a laser reflected off the + cantilever and incident on a position sensitive photodetector. + \protect\subref{fig:piezo-schematic} Schematic of a tubular piezoelectric actuator. In our AFM, the substrate is mounted on the top end of the tube, and the bottom end is fixed to the microscope body. This allows the piezo to control the relative diff --git a/src/apparatus/procedure.tex b/src/apparatus/procedure.tex index dbfb99e..25e9be2 100644 --- a/src/apparatus/procedure.tex +++ b/src/apparatus/procedure.tex @@ -39,16 +39,17 @@ multi-domain test proteins. \subfloat[][]{\asyinclude{figures/expt-sawtooth/expt-sawtooth}% \label{fig:expt-sawtooth}} % Possibly use carrion-vazquez00 figure 2 to show scale of afm tip - \caption{\subref{fig:unfolding-schematic} Schematic of the + \caption{\protect\subref{fig:unfolding-schematic} Schematic of the experimental setup for mechanical unfolding of proteins using an AFM (not to scale). An experiment starts with the tip in contact with the substrate surface, which is then moved away from the tip at a constant speed. $x_t$ is the distance traveled by the substrate, $x_c$ is the cantilever deflection, $x_u$ is the extension of the unfolded polymer, and $x_f=x_{f1}+x_{f2}$ is the - extension of the folded polymer. \subref{fig:expt-sawtooth} An - experimental force curve from stretching a ubiquitin polymer with - the rising parts of the peaks fitted to the WLC\index{WLC} model + extension of the folded polymer. + \protect\subref{fig:expt-sawtooth} An experimental force curve + from stretching a ubiquitin polymer with the rising parts of the + peaks fitted to the WLC\index{WLC} model (\cref{sec:sawsim:tension:wlc})\citep{chyan04}. The pulling speed used was $1\U{$\mu$m/s}$. The irregular features at the beginning of the curve are due to nonspecific interactions between the tip diff --git a/src/introduction/main.tex b/src/introduction/main.tex index 2fad3fd..5c06ee9 100644 --- a/src/introduction/main.tex +++ b/src/introduction/main.tex @@ -86,17 +86,18 @@ accuracy. % \hspace{.25in}% \subfloat[][]{\includegraphics[width=2in]{figures/schematic/dill97-fig4}% \label{fig:folding:landscape}} - \caption{\subref{fig:folding:pathway} A ``double T'' example of the - pathway model of protein folding, in which the protein proceeds - from the native state $N$ to the unfolded state $U$ via a series - of metastable transition states $I_1$ and $I_2$ with two ``dead - end'' states $I_1^X$ and $I_2^X$. Adapted from \citet{bedard08}. - \subref{fig:folding:landscape} The landscape model of protein - folding, in which the protein diffuses through a multi-dimensional - free energy landscape. Separate folding attempts may take many - distinct routes through this landscape on the way to the folded - state. Reproduced from \citet{dill97}. - \label{fig:folding}} + \caption{\protect\subref{fig:folding:pathway} A ``double T'' example + of the pathway model of protein folding, in which the protein + proceeds from the native state $N$ to the unfolded state $U$ via a + series of metastable transition states $I_1$ and $I_2$ with two + ``dead end'' states $I_1^X$ and $I_2^X$. Adapted from + \citet{bedard08}. + \protect\subref{fig:folding:landscape} The landscape model of + protein folding, in which the protein diffuses through a + multi-dimensional free energy landscape. Separate folding + attempts may take many distinct routes through this landscape on + the way to the folded state. Reproduced from + \citet{dill97}.\label{fig:folding}} \end{center} \end{figure} diff --git a/src/sawsim/discussion.tex b/src/sawsim/discussion.tex index 74768aa..f698578 100644 --- a/src/sawsim/discussion.tex +++ b/src/sawsim/discussion.tex @@ -54,9 +54,9 @@ low-dimensional parameter spaces). $k_{u0}=3.3\E{-4}\U{s$^{-1}$}$, $\Delta x=0.35\U{nm}$. \\ \bottomrule \end{tabular}} - \caption{\subref{tab:sawsim:domains} Model for + \caption{\protect\subref{tab:sawsim:domains} Model for I27\textsubscript{8} domain states and - \subref{tab:sawsim:transitions} transitions between them + \protect\subref{tab:sawsim:transitions} transitions between them (compare with \cref{fig:sawsim:domains}). The models and parameters are those given by \citet{carrion-vazquez99b}. \citet{carrion-vazquez99b} don't list their cantilever spring @@ -90,7 +90,7 @@ the connection between the substrate and the cantilever. \subfloat[][]{\asyinclude{figures/sim-hist/sim-hist}% \label{fig:sawsim:sim-hist}% } - \caption{\subref{fig:sawsim:sim-sawtooth} Three simulated force + \caption{\protect\subref{fig:sawsim:sim-sawtooth} Three simulated force curves from pulling a polymer of eight identical protein molecules. The simulation was carried out using the parameters: pulling speed $v=1\U{$\mu$m/s}$, cantilever spring constant @@ -106,9 +106,9 @@ the connection between the substrate and the cantilever. In experiments, detachments have been observed to occur at a variety of forces. For clarity, the green and blue curves are offset by $200$ and $400\U{pN}$ respectively. - \subref{fig:sawsim:sim-hist} The distribution of the unfolding + \protect\subref{fig:sawsim:sim-hist} The distribution of the unfolding forces from $400$ simulated force curves ($3200$ data points) - such as those shown in \subref{fig:sawsim:sim-sawtooth}. The + such as those shown in \protect\subref{fig:sawsim:sim-sawtooth}. The frequency is normalized by the total number of points, \ie, the height of each bin is equal to the number of data points in that bin divided by the total number of data @@ -399,19 +399,20 @@ from other sources. \subfloat[][]{\asyinclude{figures/v-dep/v-dep-sd}% \label{fig:sawsim:width-v-dep}% } - \caption{\subref{fig:sawsim:v-dep} The dependence of the unfolding - forces on the pulling speed for three different model protein - molecules characterized by the parameters $k_{u0}$ and $\Delta - x_u$. The polymer length is eight molecules, and each symbol is - the average of $3200$ data points. - \subref{fig:sawsim:width-v-dep} The dependence of standard + \caption{\protect\subref{fig:sawsim:v-dep} The dependence of the + unfolding forces on the pulling speed for three different model + protein molecules characterized by the parameters $k_{u0}$ and + $\Delta x_u$. The polymer length is eight molecules, and each + symbol is the average of $3200$ data points. + \protect\subref{fig:sawsim:width-v-dep} The dependence of standard deviation of the unfolding force distribution on the pulling speed - for the simulation data shown in \subref{fig:sawsim:v-dep}, using - the same symbols. The insets show the force distribution - histograms for the three proteins at the pulling speed of - $1\U{$\mu$m/s}$. The left, middle and right histograms are for - the proteins represented by the top, middle, and bottom lines in - \subref{fig:sawsim:v-dep}, + for the simulation data shown in + \protect\subref{fig:sawsim:v-dep}, using the same symbols. The + insets show the force distribution histograms for the three + proteins at the pulling speed of $1\U{$\mu$m/s}$. The left, + middle and right histograms are for the proteins represented by + the top, middle, and bottom lines in + \protect\subref{fig:sawsim:v-dep}, respectively.\label{fig:sawsim:all-v-dep}} \end{center} \end{figure} diff --git a/src/sawsim/methods.tex b/src/sawsim/methods.tex index fa872be..733b39b 100644 --- a/src/sawsim/methods.tex +++ b/src/sawsim/methods.tex @@ -81,14 +81,14 @@ root-finding algorithm. edge [bend left] node [above] {$k_2$} (D) (D) edge [bend left] node [below] {$k_2'$} (C); \end{tikzpicture}} - \caption{\subref{fig:sawsim:domain-chain} Extending a chain of - domains. One end of the chain is fixed, while the other is - extended at a constant speed. The domains are coupled with - rigid linkers, so the domains themselves must stretch to + \caption{\protect\subref{fig:sawsim:domain-chain} Extending a + chain of domains. One end of the chain is fixed, while the + other is extended at a constant speed. The domains are coupled + with rigid linkers, so the domains themselves must stretch to accomodate the extension. Compare with \cref{fig:unfolding-schematic}. - \subref{fig:sawsim:domain-states} Each domain exists in a - discrete state. At each timestep, it may transition into + \protect\subref{fig:sawsim:domain-states} Each domain exists in + a discrete state. At each timestep, it may transition into another state following a user-defined state matrix such as this one, showing a metastable transition state and an explicit ``cantilever'' domain.\label{fig:sawsim:domains}} @@ -154,11 +154,11 @@ is determine by summing the contour lengths \hspace{.25in}% \subfloat[][]{\asyinclude{figures/schematic/wlc-extension}% \label{fig:wlc-extension}} - \caption{\subref{fig:wlc-model} The wormlike chain models a - polymer as an elastic rod with persistence length $p$ and - contour length $L$. \subref{fig:wlc-extension} Force - vs.~extension for a WLC using Bustamante's interpolation - formula.\label{fig:wlc}} + \caption{\protect\subref{fig:wlc-model} The wormlike chain models + a polymer as an elastic rod with persistence length $p$ and + contour length $L$. + \protect\subref{fig:wlc-extension} Force vs.~extension for a WLC + using Bustamante's interpolation formula.\label{fig:wlc}} \end{center} \end{figure} @@ -240,13 +240,13 @@ Langevin function\citep{hatfield99}. \hspace{.25in}% \subfloat[][]{\asyinclude{figures/schematic/fjc-extension}% \label{fig:fjc-extension}} - \caption{\subref{fig:fjc-model} The freely-jointed chain models - the polymer as a series of $N$ rigid links, each of length $l$, - which are free to rotate about their joints. Each polymer state - is a random walk, and the density of states for a given - end-to-end distance is determined by the number of random walks - that have such an end-to-end distance. - \subref{fig:fjc-extension} Force vs.~extension for a + \caption{\protect\subref{fig:fjc-model} The freely-jointed chain + models the polymer as a series of $N$ rigid links, each of + length $l$, which are free to rotate about their joints. Each + polymer state is a random walk, and the density of states for a + given end-to-end distance is determined by the number of random + walks that have such an end-to-end distance. + \protect\subref{fig:fjc-extension} Force vs.~extension for a hundred-segment FJC. The WLC extension curve (with $p=l$) is shown as a dashed line for comparison.\label{fig:fjc}} \end{center} @@ -494,9 +494,10 @@ along the unfolding cordinate $x$ (\cref{fig:landscape:kramers}). % \hspace{.25in}% \subfloat[][]{\asyinclude{figures/schematic/kramers-integrand}% \label{fig:kramers:integrand}} - \caption{\subref{fig:landscape} Energy landscape schematic for - Kramers integration (compare with \cref{fig:bell-landscape}). - \subref{fig:kramers:integrand} A map of the magnitude of + \caption{\protect\subref{fig:landscape} Energy landscape schematic + for Kramers integration (compare with + \cref{fig:bell-landscape}). + \protect\subref{fig:kramers:integrand} A map of the magnitude of Kramers' integrand, with black lines tracing the integration region. The bulk of the contribution to the integral comes from the bump in the upper left, with $x$ near the boundary and $x'$ -- 2.26.2