salt/main.tex: Add 1TIT-hbond figure based on lu00b

diff --git a/src/figures/i27/1TIT-hbond.pml b/src/figures/i27/1TIT-hbond.pml
new file mode 100644 (file)
index 0000000..6771d05
--- /dev/null
+++ b/src/figures/i27/1TIT-hbond.pml
@@ -0,0 +1,131 @@
+load 1TIT.pdb
+
+# opaque white background with lots of fog
+set ray_opaque_background, on
+set transparency, 0
+bg_color white
+set depth_cue, 1
+set ray_trace_fog, 1
+set fog_start, 0
+set fog, -1000
+
+# max performance (slower)
+util.performance(0)
+# printable CMYK colors
+cmd.space('cmyk')
+
+# ball and stick display style
+#set_bond stick_color, white, (all), (all)
+#set_bond stick_radius, 0.14, (all), (all)
+#set sphere_scale, 0.25, (all)
+
+# stick-only display style
+set_bond stick_radius, 0.2, (all), (all)
+# but still use sphere for backbone-bound hydrogens
+set sphere_scale, 0.25, (all)
+
+# add hydrogens to protein
+h_add (all)
+
+# Setup selection groups
+
+select backbone, name C+O+N+CA
+select backbone_h, (elem H and neighbor name N)
+
+# N-terminus
+select n_term, resi 1
+# C-terminus
+select c_term, resi 89
+
+# sheet A
+select sheet_a, resi 3-6
+# sheet A'
+select sheet_ap, resi 9-15
+# sheet B (last few residues)
+select sheet_b, resi 24-26
+# sheet G (last few residues)
+select sheet_g, resi 83-87
+# tip and tail
+select early, resi 1-29
+select late, resi 80-89
+
+# anything in the interesting chains
+select front, (sheet_a or sheet_ap or sheet_b or sheet_g)
+select interesting, (front or late or early)
+
+# Ca-sensitive residues
+select ca_res, resn asp+glu
+select hot, (ca_res and front)
+
+# don't show anything except the backbone
+hide everything, all
+#show sticks, backbone
+#show spheres, backbone
+
+# draw hydrogen bonds
+#dist hbond, front, all, mode=2
+#dist hbond, all, front, mode=2
+#dist hbond, all, all, mode=2
+#dist hbond, front, front, mode=2
+# manually match lu00
+distance hbond_a, (resi 3 and name O), (resi 26 and backbone_h), mode=0
+distance hbond_b, (resi 6 and backbone_h), (resi 24 and name O), mode=0
+distance hbond_c, (resi 6 and name O), (resi 24 and backbone_h), mode=0
+distance hbond_d, (resi 9 and name O), (resi 83 and backbone_h), mode=0
+distance hbond_e, (resi 11 and backbone_h), (resi 83 and name O), mode=0
+distance hbond_f, (resi 13 and backbone_h), (resi 85 and name O), mode=0
+distance hbond_g, (resi 13 and name O), (resi 87 and backbone_h), mode=0
+distance hbond_h, (resi 15 and backbone_h), (resi 87 and name O), mode=0
+# but don't label the distances
+hide labels
+
+# decorate selections
+show sticks, backbone
+set_bond stick_radius, 0.05, (all), (all)
+set_bond stick_radius, 0.2, (interesting), (interesting)
+#show spheres, (backbone and interesting)
+show spheres, (front and backbone_h)
+color white, all
+color lightblue, early
+color lightpink, late
+color brown, n_term
+color cyan, c_term
+color br0, sheet_a
+color br2, sheet_ap
+color br4, sheet_b
+color br6, sheet_g
+color red, (hot and resn asp)
+color green, (hot and resn glu)
+color yellow, hbond_a
+color yellow, hbond_b
+color yellow, hbond_c
+color yellow, hbond_d
+color yellow, hbond_e
+color yellow, hbond_f
+color yellow, hbond_g
+color yellow, hbond_h
+
+# zoom so molecule fills window
+set_view (\
+     1.000000000,    0.000000000,    0.000000000,\
+     0.000000000,    0.087155743,    0.996194698,\
+     0.000000000,   -0.996194698,   -0.087155743,\
+     0.000000000,   -5.000000000,  -40.000000000,\
+     0.043053962,    0.000000000,    4.578000069,\
+    20.000000000,   60.000000000,   45.000000000 )
+# view matrix (from pymol.viewing.get_view)
+#   3x3 matrix rotating model space to camera space
+#   1x3 origin of rotation relative to camera in camera space
+#   1x3 origin of rotation relative to camera in model space
+#   1x1 front plane distance from the camera
+#   1x1 rear plane distance from the camera
+#   1x1 orthoscopic flag (+/-) and field of view (if abs(value) > 1)
+# The camera always looks down -Z with its +X left and its +Y down.
+# Therefore, in the default view, model +X is to the observer\'s
+# right, +Y is upward, and +Z points toward the observer.
+#
+# To zoom, tweak the field-of-view setting, decreasing to zoom in.
+
+# render with 640 pixel width
+png 1TIT-hbond.png, width=640
+quit

diff --git a/src/salt/main.tex b/src/salt/main.tex
index 135b80b5f6b5ac0bdfacae2135fa1684e2f15684..a6ff6e856acf2279bd7e11f0f9c101ed45c6cf56 100644 (file)
--- a/src/salt/main.tex
+++ b/src/salt/main.tex
@@ -19,8 +19,20 @@ aspartic and glutamic acid groups tend to have a strong affinity for
 cations while argenine has a strong affinity for the
 \Cl\ anion\citep{friedman11}.  Of these amino acids, only glutamic
 acid occurs in the key hydrogen bond regions responsible for I27
-unfolding\citep{lu00b}.  \NaCl\ has also been shown to decrease
-hydrogen bonding\citep{zidar11}.
+unfolding\citep{lu00b} (\cref{fig:I27:H-bonds}).  \NaCl\ has also been
+shown to decrease hydrogen bonding\citep{zidar11}.
+
+\begin{figure}
+  \begin{center}
+    \includegraphics[width=0.5\textwidth]{figures/i27/1TIT-hbond}
+    \caption{The backbone of I27 showing the eight key hydogen bonds
+      responsible for the critical unfolding force.  Glutamic acids
+      are highlighted in green.  Based on \xref{lu00b}{figure}{1b}.
+      For a ribbon diagram of I27 showing the $\beta$-sheets, see
+      \cref{fig:I27}.  This figure was also generated with
+      \citetalias{pymol}.\label{fig:I27:H-bonds}}
+  \end{center}
+\end{figure}
 
 We added $0.5\U{M}$ \CaCl\ to our standard PBS
 (\cref{sec:sample-preparation}), which is much larger than