From ee5bcd36ffa6071a9b2f9ae6c69284e8d3679e9e Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 17 Feb 2010 19:22:21 -0500 Subject: [PATCH] Broke the figures out into their own src subdirectory. They used to live under the different chapters, but the new structure will make it easier to share figure-generation code between chapters. --- tex/src/Makefile | 2 +- tex/src/apparatus/Makefile | 3 + tex/src/cantilever-calib/Makefile | 15 +-- .../cantilever-calib/contour_integration.tex | 2 +- tex/src/cantilever/Makefile | 3 + tex/src/contour-space/Makefile | 3 + tex/src/{sawsim => }/figures/Makefile | 5 +- .../figures/calibration-concept-map/Makefile | 7 ++ .../calibration-concept-map}/concept_map.dot | 0 tex/src/figures/contour/Makefile | 7 ++ .../contour}/contour.asy | 0 .../expt-sawtooth}/Makefile | 0 .../{sawsim => }/figures/expt-sawtooth/NOTES | 0 .../{sawsim => }/figures/expt-sawtooth/expt.d | 0 .../figures/expt-sawtooth/plot.gp | 0 .../figures/expt-sawtooth/sawmodel.xml | 0 .../fig3.ppm | Bin .../fig3a.clicks | 0 .../fig3a.data | 0 .../fig3a.data.loglog | 0 .../fig3a.summary | 0 .../fit.log | 0 .../king_expt.data | 0 .../king_extrap.data | 0 .../king_sim-566.data | 0 .../loglog_to_normal.py | 0 .../sim-hist => figures/fit-space}/Makefile | 0 tex/src/{sawsim => }/figures/fit-space/data | 0 .../figures/fit-space/extract_fit_valley.py | 0 .../{sawsim => }/figures/fit-space/fit.log | 0 .../figures/fit-space/fit_valley.data | 0 .../figures/fit-space/king_vs_best.gp | 0 .../figures/fit-space/king_vs_best.png | Bin tex/src/{sawsim => }/figures/fit-space/means | 0 .../{sawsim => }/figures/fit-space/means.gp | 0 .../{sawsim => }/figures/fit-space/plot.gp | 0 .../figures/folded-model-hists/fig.pdf | Bin .../figures/kappa-sawteeth/Makefile | 0 .../figures/kappa-sawteeth/data-0.001 | 0 .../figures/kappa-sawteeth/data-0.01 | 0 .../figures/kappa-sawteeth/data-0.05 | 0 .../figures/kappa-sawteeth/data-0.1 | 0 .../figures/kappa-sawteeth/data-0.5 | 0 .../figures/kappa-sawteeth/data-1 | 0 .../figures/kappa-sawteeth/data-10 | 0 .../figures/kappa-sawteeth/plot.gp | 0 .../{sawsim => }/figures/order-dep/Makefile | 0 .../figures/order-dep/data/hist3i.hist | 0 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tex/src/cantilever/Makefile create mode 100644 tex/src/contour-space/Makefile rename tex/src/{sawsim => }/figures/Makefile (66%) create mode 100644 tex/src/figures/calibration-concept-map/Makefile rename tex/src/{cantilever-calib/dot => figures/calibration-concept-map}/concept_map.dot (100%) create mode 100644 tex/src/figures/contour/Makefile rename tex/src/{cantilever-calib => figures/contour}/contour.asy (100%) rename tex/src/{sawsim/figures/sim-sawtooth => figures/expt-sawtooth}/Makefile (100%) rename tex/src/{sawsim => }/figures/expt-sawtooth/NOTES (100%) rename tex/src/{sawsim => }/figures/expt-sawtooth/expt.d (100%) rename tex/src/{sawsim => }/figures/expt-sawtooth/plot.gp (100%) rename tex/src/{sawsim => }/figures/expt-sawtooth/sawmodel.xml (100%) rename tex/src/{sawsim => }/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3.ppm (100%) rename tex/src/{sawsim => }/figures/fit-space/Best_2002_detailed_unfolding_pathway/fig3a.clicks (100%) rename tex/src/{sawsim => 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mode 120000 tex/src/sawsim/fit-space.pdf delete mode 120000 tex/src/sawsim/kappa-sawteeth.pdf delete mode 120000 tex/src/sawsim/order-dep.pdf delete mode 120000 tex/src/sawsim/schematic.pdf delete mode 120000 tex/src/sawsim/sim-hist.pdf delete mode 120000 tex/src/sawsim/sim-sawtooth.pdf delete mode 120000 tex/src/sawsim/v-dep-sd.pdf delete mode 120000 tex/src/sawsim/v-dep.pdf create mode 100644 tex/src/temperature-theory/Makefile create mode 100644 tex/src/temperature/Makefile create mode 100644 tex/src/tension/Makefile create mode 100644 tex/src/unfolding/Makefile diff --git a/tex/src/Makefile b/tex/src/Makefile index e99154c..b747772 100644 --- a/tex/src/Makefile +++ b/tex/src/Makefile @@ -1,5 +1,5 @@ SUBDIRS = packages apparatus cantilever cantilever-calib contour-space \ - future introduction sawsim temperature temperature-theory \ + figures future introduction sawsim temperature temperature-theory \ tension unfolding unfolding-distributions viscocity all : diff --git a/tex/src/apparatus/Makefile b/tex/src/apparatus/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/apparatus/Makefile @@ -0,0 +1,3 @@ +all : + +clean : diff --git a/tex/src/cantilever-calib/Makefile b/tex/src/cantilever-calib/Makefile index 0c98a97..a260214 100644 --- a/tex/src/cantilever-calib/Makefile +++ b/tex/src/cantilever-calib/Makefile @@ -1,16 +1,3 @@ -GEN_FILES = contour.pdf #dot/concept_map.png - -all : $(GEN_FILES) +all : clean : - rm -f $(GEN_FILES) - $(MAKE) -C test clean - -check : - $(MAKE) -C test all - -contour.pdf : - asy -f pdf contour.asy - -dot/concept_map.png : - dot -Tpng dot/concept_map.dot > $@ diff --git a/tex/src/cantilever-calib/contour_integration.tex b/tex/src/cantilever-calib/contour_integration.tex index 3f3df7b..591b575 100644 --- a/tex/src/cantilever-calib/contour_integration.tex +++ b/tex/src/cantilever-calib/contour_integration.tex @@ -2,7 +2,7 @@ \begin{figure} \begin{centering} - \includegraphics[width=0.3\textwidth]{cantilever-calib/contour} \\ + \includegraphics[width=0.3\textwidth]{figures/contour/contour} \\ \caption{Integral contour \C\ enclosing the upper half plane.} \label{f.UHP_contour} \end{centering} diff --git a/tex/src/cantilever/Makefile b/tex/src/cantilever/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/cantilever/Makefile @@ -0,0 +1,3 @@ +all : + +clean : diff --git a/tex/src/contour-space/Makefile b/tex/src/contour-space/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/contour-space/Makefile @@ -0,0 +1,3 @@ +all : + +clean : diff --git a/tex/src/sawsim/figures/Makefile b/tex/src/figures/Makefile similarity index 66% rename from tex/src/sawsim/figures/Makefile rename to tex/src/figures/Makefile index 0030b18..adafb9c 100644 --- a/tex/src/sawsim/figures/Makefile +++ b/tex/src/figures/Makefile @@ -1,5 +1,6 @@ -SUBDIRS = expt-sawtooth fit-space kappa-sawteeth order-dep \ - schematic sim-hist sim-sawtooth v-dep +SUBDIRS = expt-sawtooth fit-space contour kappa-sawteeth order-dep \ + schematic sim-hist sim-sawtooth v-dep \ + # calibration-concept-map all : @for i in $(SUBDIRS); do \ diff --git a/tex/src/figures/calibration-concept-map/Makefile b/tex/src/figures/calibration-concept-map/Makefile new file mode 100644 index 0000000..b9f8fec --- /dev/null +++ b/tex/src/figures/calibration-concept-map/Makefile @@ -0,0 +1,7 @@ +all : concept_map.png + +clean : + rm -f concept_map.png + +concept_map.png : + dot -Tpng concept_map.dot > $@ diff --git a/tex/src/cantilever-calib/dot/concept_map.dot b/tex/src/figures/calibration-concept-map/concept_map.dot similarity index 100% rename from tex/src/cantilever-calib/dot/concept_map.dot rename to tex/src/figures/calibration-concept-map/concept_map.dot diff --git a/tex/src/figures/contour/Makefile b/tex/src/figures/contour/Makefile new file mode 100644 index 0000000..8936b13 --- /dev/null +++ b/tex/src/figures/contour/Makefile @@ -0,0 +1,7 @@ +all : contour.pdf + +clean : + rm -f contour.pdf + +contour.pdf : + asy -f pdf contour.asy diff --git a/tex/src/cantilever-calib/contour.asy b/tex/src/figures/contour/contour.asy similarity index 100% rename from tex/src/cantilever-calib/contour.asy rename to tex/src/figures/contour/contour.asy diff --git a/tex/src/sawsim/figures/sim-sawtooth/Makefile b/tex/src/figures/expt-sawtooth/Makefile similarity index 100% rename from tex/src/sawsim/figures/sim-sawtooth/Makefile rename to tex/src/figures/expt-sawtooth/Makefile diff --git a/tex/src/sawsim/figures/expt-sawtooth/NOTES b/tex/src/figures/expt-sawtooth/NOTES similarity index 100% rename from tex/src/sawsim/figures/expt-sawtooth/NOTES rename to tex/src/figures/expt-sawtooth/NOTES diff --git a/tex/src/sawsim/figures/expt-sawtooth/expt.d b/tex/src/figures/expt-sawtooth/expt.d similarity index 100% rename from tex/src/sawsim/figures/expt-sawtooth/expt.d rename to tex/src/figures/expt-sawtooth/expt.d diff --git 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: diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex index 927a76c..47ed3fa 100644 --- a/tex/src/introduction/main.tex +++ b/tex/src/introduction/main.tex @@ -112,9 +112,9 @@ single molecule mechanical unfolding experiments. \begin{figure} \begin{center} -\subfloat[][]{\includegraphics{sawsim/schematic}\label{fig:schematic}} +\subfloat[][]{\includegraphics{figures/schematic/unfolding}\label{fig:schematic}} %\hspace{.25in}% -\subfloat[][]{\includegraphics{sawsim/expt-sawtooth}\label{fig:expt-sawtooth}} +\subfloat[][]{\includegraphics{figures/expt-sawtooth/fig}\label{fig:expt-sawtooth}} \caption{(a) 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 diff --git a/tex/src/sawsim/Makefile b/tex/src/sawsim/Makefile index 91ae5b1..a1f4f4c 100644 --- a/tex/src/sawsim/Makefile +++ b/tex/src/sawsim/Makefile @@ -1,10 +1,3 @@ -all : figures +all : -clean : figures-clean - -.PHONY : figures -figures : - $(MAKE) --directory figures all - -figures-clean : - $(MAKE) --directory figures clean +clean : diff --git a/tex/src/sawsim/discussion.tex b/tex/src/sawsim/discussion.tex index 6e65fd6..151aa41 100644 --- a/tex/src/sawsim/discussion.tex +++ b/tex/src/sawsim/discussion.tex @@ -23,9 +23,9 @@ deviation of $25\U{pN}$. \begin{figure} \vspace{-1in} \begin{center} -\subfloat[][]{\includegraphics{sawsim/sim-sawtooth}\label{fig:sawsim:sim-sawtooth}% +\subfloat[][]{\includegraphics{figures/sim-sawtooth/fig}\label{fig:sawsim:sim-sawtooth}% }\\ -\subfloat[][]{\includegraphics{sawsim/sim-hist}\label{fig:sawsim:sim-hist}% +\subfloat[][]{\includegraphics{figures/sim-hist/fig}\label{fig:sawsim:sim-hist}% } \caption{(a) Three simulated force curves from pulling a polymer of eight identical protein molecules. The simulation was carried out @@ -152,25 +152,26 @@ quite different for the same protein because of the differences in unfolding order and polymer length. \begin{figure} -\begin{center} -\includegraphics{sawsim/order-dep} -\caption{The dependence of the unfolding force on the temporal - unfolding order for four polymers with $4$, $8$, $12$, and $16$ - molecules of identical proteins. Each point in the figure is the - average of $400$ data points. The first point in each curve - represents the average of only the first peak in each of the $400$ - simulated force curves, the second point represents the average of - only the second peak, and so on. The solid lines are fits of - \cref{eq:sawsim:order-dep} to the simulated data, with best fit - $\kappa_\text{WLC}=203$, $207$, $161$, and $157\U{pN/nm}$, - respectively, for lengths $4$ through $16$. The insets show the - force distributions of the first, fourth, and eighth peaks, left to - right, for the polymer with eight protein molecules. The parameters - used for generating the data were the same as those used for - \cref{fig:sawsim:sim-sawtooth}, except the polymer length, and the - histograms in the insets were normalized in the same way as in - \cref{fig:sawsim:sim-hist}.\label{fig:sawsim:order-dep}} -\end{center} + \begin{center} + \includegraphics{figures/order-dep/fig} + \caption{The dependence of the unfolding force on the temporal + unfolding order for four polymers with $4$, $8$, $12$, and $16$ + molecules of identical proteins. Each point in the figure is the + average of $400$ data points. The first point in each curve + represents the average of only the first peak in each of the $400$ + simulated force curves, the second point represents the average of + only the second peak, and so on. The solid lines are fits of + \cref{eq:sawsim:order-dep} to the simulated data, with best fit + $\kappa_\text{WLC}=203$, $207$, $161$, and $157\U{pN/nm}$, + respectively, for lengths $4$ through $16$. The insets show the + force distributions of the first, fourth, and eighth peaks, left + to right, for the polymer with eight protein molecules. The + parameters used for generating the data were the same as those + used for \cref{fig:sawsim:sim-sawtooth}, except the polymer + length, and the histograms in the insets were normalized in the + same way as in + \cref{fig:sawsim:sim-hist}.\label{fig:sawsim:order-dep}} + \end{center} \end{figure} \subsection{The effect of polymer inhomogeneity} @@ -236,7 +237,7 @@ to WLC or other polymer models (\cref{fig:expt-sawtooth}). \begin{figure} \begin{center} -\includegraphics{sawsim/kappa-sawteeth} +\includegraphics{figures/kappa-sawteeth/fig} \caption{Simulated force curves obtained from pulling a polymer with eight protein molecules using cantilevers with different force constants $\kappa_c$. Parameters used in generating these curves @@ -319,37 +320,39 @@ the unfolding force distribution, as well as any relevant information about the protein from other sources. \begin{figure} -\begin{center} -\subfloat[][]{\includegraphics{sawsim/v-dep}\label{fig:sawsim:v-dep}% -} \\ -\subfloat[][]{\includegraphics{sawsim/v-dep-sd}\label{fig:sawsim:width-v-dep}% -} -\caption{(a) 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. (b) The dependence of standard deviation of the unfolding - force distribution on the pulling speed for the simulation data - shown in (a), 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 (a), - respectively.\label{fig:sawsim:all-v-dep}} -\end{center} + \begin{center} + \subfloat[][]{\includegraphics{figures/v-dep/fig}% + \label{fig:sawsim:v-dep}% + } \\ + \subfloat[][]{\includegraphics{figures/v-dep/fig-sd}% + \label{fig:sawsim:width-v-dep}% + } + \caption{(a) 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. (b) The dependence of standard deviation of the unfolding + force distribution on the pulling speed for the simulation data + shown in (a), 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 (a), respectively.\label{fig:sawsim:all-v-dep}} + \end{center} \end{figure} \begin{figure} -\begin{center} -\includegraphics{sawsim/fit-space} -\caption{Fit quality between an experimental data set and simulated - data sets obtained using various values of unfolding rate parameters - $k_{u0}$ and $\Delta x_u$. The experimental data are from octameric - ubiquitin pulled at $1\U{$\mu$m/s}$\citep{chyan04}, and the other - model parameters are the same as those in \cref{fig:sawsim:sim-all}. The - best fit parameters are $\Delta x_u=0.17\U{nm}$ and - $k_{u0}=1.2\E{-2}\U{s$^{-1}$}$. The simulation histograms were - built from $400$ pulls at for each parameter pair. The color scale - shown on the right is $log_{10}(D_\text{JS})$. -\label{fig:sawsim:fit-space}} -\end{center} + \begin{center} + \includegraphics{figures/fit-space/fig} + \caption{Fit quality between an experimental data set and simulated + data sets obtained using various values of unfolding rate + parameters $k_{u0}$ and $\Delta x_u$. The experimental data are + from octameric ubiquitin pulled at $1\U{$\mu$m/s}$\citep{chyan04}, + and the other model parameters are the same as those in + \cref{fig:sawsim:sim-all}. The best fit parameters are $\Delta + x_u=0.17\U{nm}$ and $k_{u0}=1.2\E{-2}\U{s$^{-1}$}$. The + simulation histograms were built from $400$ pulls at for each + parameter pair. The color scale shown on the right is + $log_{10}(D_\text{JS})$.\label{fig:sawsim:fit-space}} + \end{center} \end{figure} diff --git a/tex/src/sawsim/expt-sawtooth.pdf b/tex/src/sawsim/expt-sawtooth.pdf deleted file mode 120000 index 8bceed8..0000000 --- a/tex/src/sawsim/expt-sawtooth.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/expt-sawtooth/fig.pdf \ No newline at end of file diff --git a/tex/src/sawsim/figures/README b/tex/src/sawsim/figures/README deleted file mode 100644 index a519c6f..0000000 --- a/tex/src/sawsim/figures/README +++ /dev/null @@ -1,23 +0,0 @@ -Tiffs (.tif) for raster -EPS/PDF (.eps/.pdf) for vector - -Figure sizes: - 1 column : 90mm wide - 1.5 columns: 140mm wide - 2 columns : 190mm wide - -Raster resolutions - Halftone/Gray/RGB: 300dpi - Line art : 1000dpi - Combination art : 500dpi - -EPS: include preview/thumbnail - -Artwork lettering: 7pt for normal text (rule of thumb). -Embed fonts, use Arial, Courier, Times, Symbol. - (I can't figure out how to embed fonts in gnuplot's PDF terminal, - but times shouldn't change all that much, so don't worry about - it...) - -Naming: - fig1.tif, etc. ... diff --git a/tex/src/sawsim/fit-space.pdf b/tex/src/sawsim/fit-space.pdf deleted file mode 120000 index e90d165..0000000 --- a/tex/src/sawsim/fit-space.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/fit-space/fig.pdf \ No newline at end of file diff --git a/tex/src/sawsim/kappa-sawteeth.pdf b/tex/src/sawsim/kappa-sawteeth.pdf deleted file mode 120000 index d283893..0000000 --- a/tex/src/sawsim/kappa-sawteeth.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/kappa-sawteeth/fig.pdf \ No newline at end of file diff --git a/tex/src/sawsim/order-dep.pdf b/tex/src/sawsim/order-dep.pdf deleted file mode 120000 index 190675b..0000000 --- a/tex/src/sawsim/order-dep.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/order-dep/fig.pdf \ No newline at end of file diff --git a/tex/src/sawsim/schematic.pdf b/tex/src/sawsim/schematic.pdf deleted file mode 120000 index eb7a025..0000000 --- a/tex/src/sawsim/schematic.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/schematic/unfolding.pdf \ No newline at end of file diff --git a/tex/src/sawsim/sim-hist.pdf b/tex/src/sawsim/sim-hist.pdf deleted file mode 120000 index 0d3dfc3..0000000 --- a/tex/src/sawsim/sim-hist.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/sim-hist/fig.pdf \ No newline at end of file diff --git a/tex/src/sawsim/sim-sawtooth.pdf b/tex/src/sawsim/sim-sawtooth.pdf deleted file mode 120000 index ed1d2a8..0000000 --- a/tex/src/sawsim/sim-sawtooth.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/sim-sawtooth/fig.pdf \ No newline at end of file diff --git a/tex/src/sawsim/v-dep-sd.pdf b/tex/src/sawsim/v-dep-sd.pdf deleted file mode 120000 index ffb79d8..0000000 --- a/tex/src/sawsim/v-dep-sd.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/v-dep/fig-sd.pdf \ No newline at end of file diff --git a/tex/src/sawsim/v-dep.pdf b/tex/src/sawsim/v-dep.pdf deleted file mode 120000 index 0f2e340..0000000 --- a/tex/src/sawsim/v-dep.pdf +++ /dev/null @@ -1 +0,0 @@ -figures/v-dep/fig.pdf \ No newline at end of file diff --git a/tex/src/temperature-theory/Makefile b/tex/src/temperature-theory/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/temperature-theory/Makefile @@ -0,0 +1,3 @@ +all : + +clean : diff --git a/tex/src/temperature/Makefile b/tex/src/temperature/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/temperature/Makefile @@ -0,0 +1,3 @@ +all : + +clean : diff --git a/tex/src/tension/Makefile b/tex/src/tension/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/tension/Makefile @@ -0,0 +1,3 @@ +all : + +clean : diff --git a/tex/src/unfolding/Makefile b/tex/src/unfolding/Makefile new file mode 100644 index 0000000..a1f4f4c --- /dev/null +++ b/tex/src/unfolding/Makefile @@ -0,0 +1,3 @@ +all : + +clean : -- 2.26.2