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Organize stereospecific Figure #36

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May 12, 2015
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Organize stereospecific Figure #36

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Binary file removed DATAreportediINblog/stereospecificOPs.pdf
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50 changes: 38 additions & 12 deletions Fig/Makefile
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Expand Up @@ -4,6 +4,7 @@
# For each figure, a serie of variables can be set (mainly for the location of the script
# and for the path of the data files). The rule to generate the figure is below those.
# The idea is to only re-generate the output when the dependencies (script or data) are changed.
# BE AWARE, all variables must have different names otherwise Makefile will fail.
#
# At the beginning of the Makefile, the output filename can be also changed.
#
Expand All @@ -13,7 +14,7 @@
## Figure filenames ##
######################
dehydrationPN = dehydrationPN.pdf

stereospecific = stereospecificOPs.pdf


# Generate TARGETs from all filenames
Expand All @@ -29,26 +30,51 @@ all: $(TARGETS)

# Variables
# =========
SCRIPT = scripts/plotDehydrationPNvector.gpl
DATA_BERGER = ../DATAreportediINblog/POPC/dehydration/PN-vector/Berger-298K.dat
DATA_BERGER_DLPC = ../DATAreportediINblog/DLPC/dehydration/PN-vector/Berger-300K.dat
DATA_MACROG = ../DATAreportediINblog/POPC/dehydration/PN-vector/MacRog-310K.dat
DATA_CHARMM36 = ../DATAreportediINblog/POPC/dehydration/PN-vector/CHARMM36-303K.dat
DATA_GAFF = ../DATAreportediINblog/POPC/dehydration/PN-vector/GAFF-303K.dat
SCRIPT_DEHY = scripts/plotDehydrationPNvector.gpl
DEHY_BERGER = ../DATAreportediINblog/POPC/dehydration/PN-vector/Berger-298K.dat
DEHY_BERGER_DLPC = ../DATAreportediINblog/DLPC/dehydration/PN-vector/Berger-300K.dat
DEHY_MACROG = ../DATAreportediINblog/POPC/dehydration/PN-vector/MacRog-310K.dat
DEHY_CHARMM36 = ../DATAreportediINblog/POPC/dehydration/PN-vector/CHARMM36-303K.dat
DEHY_GAFF = ../DATAreportediINblog/POPC/dehydration/PN-vector/GAFF-303K.dat

# Rule
# ====
$(dehydrationPN): $(SCRIPT) $(DATA_BERGER) $(DATA_MACROG) $(DATA_CHARMM36) $(DATA_GAFF)
gnuplot -e "OUTPUTFILE='$@'" -e "DATA_BERGER='$(DATA_BERGER)'" -e "DATA_BERGER_DLPC='$(DATA_BERGER_DLPC)'" \
-e "DATA_MACROG='$(DATA_MACROG)'" -e "DATA_CHARMM36='$(DATA_CHARMM36)'" \
-e "DATA_GAFF='$(DATA_GAFF)'" \
$(SCRIPT)
$(dehydrationPN): $(SCRIPT_DEHY) $(DEHY_BERGER) $(DEHY_BERGER_DLPC) $(DEHY_MACROG) $(DEHY_CHARMM36) $(DEHY_GAFF)
gnuplot -e "OUTPUTFILE='$@'" -e "DATA_BERGER='$(DEHY_BERGER)'" -e "DATA_BERGER_DLPC='$(DEHY_BERGER_DLPC)'" \
-e "DATA_MACROG='$(DEHY_MACROG)'" -e "DATA_CHARMM36='$(DEHY_CHARMM36)'" \
-e "DATA_GAFF='$(DEHY_GAFF)'" \
$(SCRIPT_DEHY)

#------------#
# end Figure #
#------------#


#----------------------------------------------#
# Figure regarding the sterero specificity #
#----------------------------------------------#

# Variables
# =========
SCRIPT_STER = scripts/plotWithStereospecificity.gpl
STER_EXP = ../DATAreportediINblog/POPC-for-stereospecific/EXP-Ferreira2013.dat
STER_BERGER = ../DATAreportediINblog/POPC-for-stereospecific/BERGER-298K_recalculated-22-04-15.dat
STER_MACROG = ../DATAreportediINblog/POPC-for-stereospecific/MACROG-310K_recalculated-29-04-15.dat
STER_CHARMM36 = ../DATAreportediINblog/POPC-for-stereospecific/CHARMM36-303K_blogged-01-12-14.dat
STER_GAFF = ../DATAreportediINblog/POPC-for-stereospecific/GAFF-303K_blogged-12-11-14.dat

# Rule
# ====
$(stereospecific): $(SCRIPT_STER) $(STER_EXP) $(STER_BERGER) $(STER_MACROG) $(STER_CHARMM36) $(STER_GAFF)
gnuplot -e "OUTPUTFILE='$@'" -e "DATA_EXP='$(STER_EXP)'" -e "DATA_BERGER='$(STER_BERGER)'" \
-e "DATA_MACROG='$(STER_MACROG)'" -e "DATA_CHARMM36='$(STER_CHARMM36)'" \
-e "DATA_GAFF='$(STER_GAFF)'" \
$(SCRIPT_STER)

#------------#
# end Figure #
#------------#



clean:
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17 changes: 6 additions & 11 deletions ...rtediINblog/plotWithStereospecificity.gpl → Fig/scripts/plotWithStereospecificity.gpl
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@@ -1,5 +1,5 @@
set term pdfcairo enhanced rounded color dashed dashlength 1 size 10cm, 21cm #16.2cm
set out "stereospecificOPs.pdf"
set out OUTPUTFILE

# write name of the blog on the plot:
# set label 1 right at screen 0.982,0.995 "nmrlipids.blogspot.fi" font ",9" tc rgb "gray"
Expand Down Expand Up @@ -49,17 +49,12 @@ set linetype 24 lt 1 lw w lc rgb "#FFD300" # for GAFF
set linetype 30 lt 1 lw w lc rgb "#00A368" # for MacRog

plot [0.5:7.5][0.152659:-0.26] \
"./POPC-for-stereospecific/BERGER-298K_recalculated-22-04-15.dat" u ($1-0.4):($2):($3) w ye lt 21 pt 7 ps r \
t "{298K} Berger", \
"./POPC-for-stereospecific/MACROG-310K_recalculated-29-04-15.dat" u ($1-0.2):($2):($3) w ye lt 30 pt 7 ps r \
t "{310K} MacRog", \
"./POPC-for-stereospecific/EXP-Ferreira2013.dat" u ($1):($2):($3) w ye lt 101 pt 7 ps 1.5*r \
t "300K ^{_{^{13}}}C-NMR", \
DATA_BERGER u ($1-0.4):($2):($3) w ye lt 21 pt 7 ps r t "{298K} Berger", \
DATA_MACROG u ($1-0.2):($2):($3) w ye lt 30 pt 7 ps r t "{310K} MacRog", \
DATA_EXP u ($1):($2):($3) w ye lt 101 pt 7 ps 1.5*r t "300K ^{_{^{13}}}C-NMR", \
x w p ls 1 ps 0 t " ", \
"./POPC-for-stereospecific/GAFF-303K_blogged-12-11-14.dat" u ($1+0.2):($2):($3) w ye lt 24 pt 7 ps r \
t "{303K} GAFFlipid", \
"./POPC-for-stereospecific/CHARMM36-303K_blogged-01-12-14.dat" u ($1+0.4):($2):($3) w ye lt 23 pt 7 ps r \
t "@{\\ \\ \"}&{303K} CHARMM36"
DATA_GAFF u ($1+0.2):($2):($3) w ye lt 24 pt 7 ps r t "{303K} GAFFlipid", \
DATA_CHARMM36 u ($1+0.4):($2):($3) w ye lt 23 pt 7 ps r t "@{\\ \\ \"}&{303K} CHARMM36"



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Binary file added Fig/stereospecificOPs.pdf
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Binary file modified HGmodelMANUSCRIPT/HGmodel_ACStemplate.pdf
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2 changes: 1 addition & 1 deletion HGmodelMANUSCRIPT/HGmodel_ACStemplate.tex
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Expand Up @@ -596,7 +596,7 @@ \subsection{Full hydration: Experimental order parameters for the glycerol backb
and the stereospecific labeling from~\cite{gally81}, and shown in Fig.~\ref{HGorderparameters2}.
\begin{figure*}[]
\centering
\includegraphics[width=8.6cm]{../DATAreportediINblog/stereospecificOPs.pdf} \\
\includegraphics[width=8.6cm]{../Fig/stereospecificOPs.pdf} \\
\caption{\label{HGorderparameters2}
Order parameteres for POPC glycerol and choline groups
from simulations with Berger-POPC-07, MacRog, GAFFlipid, and CHARMM36 force fields
Expand Down