# LaTeX2HTML 2002-2-1 (1.71)
# Associate images original text with physical files.


$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut_licotube}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="658" HEIGHT="364" BORDER="0"
 SRC="|."$dir".q|img14.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut_licotube}
}
\end{center}
\end{figure}">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslagorithmthatinthiscaseshowsonlyfourofthefive{beta{strands.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="145" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img15.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...at in this case shows only four of the five
$\beta$ strands.}
\end{minipage} }">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslacomestothisconfiguration(Eachframestepcorrespondsto10ps.)}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="131" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img47.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...o this configuration (Each frame step corresponds to 10 ps. )}
\end{minipage} }">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslamictheeffectofpullingontheCterminuswiththiskindoflinkage.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="131" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img51.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...ffect of pulling on the C terminus with this kind of linkage.}
\end{minipage} }">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6ePDBfile.Otherkeywords,suchasresidue,areconsistentwiththePDBfile.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="110" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img52.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...
keywords, such as residue, are consistent with the PDB file.}
\end{minipage} }">|; 

$key = q/framebox[0.9textwidth]{partabular{{ll}{ttexpr}{itexpression}&--evaluatesamathematicalexpressiontabular{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="501" HEIGHT="30" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img26.gif"
 ALT="\framebox[0.9\textwidth]{
\par
\begin{tabular}{ll}
{\tt expr} {\it expression} &amp; - evaluates a mathematical expression
\end{tabular}
}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6.FormoreinformationoftheVMDstartupfiles,refertotheVMDuser'sguide.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="94" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img42.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...tion of the VMD startup files, refer to the
VMD user's guide.}
\end{minipage} }">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslastheproteinachieveproperfoldingandincreasesit'sstability.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="145" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img32.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
... protein achieve proper folding and increases it's stability.}
\end{minipage} }">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslahesizeofthewaterboxdecreasestoobtaintherightwaterdensity.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="197" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img60.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...f the water box decreases to obtain the right water
density. }
\end{minipage} }">|; 

$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_unit01_001}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="600" HEIGHT="500" BORDER="0"
 SRC="|."$dir".q|img5.gif"
 ALT="\begin{figure}\begin{center}
\includegraphics[scale=0.5]{pictures/tut_unit01_001}
\end{center}
\end{figure}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6hbondasacylinder,butthesphereradiuscannotbemodifiedindependently.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="129" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img12.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...nder, but the sphere radius cannot be modified independently.}
\end{minipage} }">|; 

$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_unit01_006}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="423" HEIGHT="630" BORDER="0"
 SRC="|."$dir".q|img18.gif"
 ALT="\begin{figure}\begin{center}
\includegraphics[scale=0.5]{pictures/tut_unit01_006}
\end{center}
\end{figure}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6stemthatyouhavecomputedandwhichisnotsupportedout-of-the-boxbyVMD.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="181" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img28.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...ve computed and which is not supported out-of-the-box by VMD.}
\end{minipage} }">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_tkcon}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="501" HEIGHT="237" BORDER="0"
 SRC="|."$dir".q|img24.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut2_tkcon}
}
\end{center}
\end{figure}">|; 

$key = q/framebox[0.9textwidth]{partabular{{ll}{ttatomselectmacro}{itname}{itselection}&--createsamacrofor{itselection}tabular{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="501" HEIGHT="30" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img40.gif"
 ALT="\framebox[0.9\textwidth]{
\par
\begin{tabular}{ll}
{\tt atomselect macro }...
...e} {\it selection} &amp; -
creates a macro for {\it selection}
\end{tabular}
}">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslangtwomolecules,likeinUnit2,{t{labelsthemolecules).}minipage{};MSF=1.6;TAGS=R;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="204" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img59.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...ng two molecules, like in Unit 2, $t$ labels the molecules).}
\end{minipage} }">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut_label_window}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="370" HEIGHT="359" BORDER="0"
 SRC="|."$dir".q|img55.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut_label_window}
}
\end{center}
\end{figure}">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslaWewilltalksomemoreabouttherelevanceofthisphenomenonlater.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="131" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img48.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
... talk some more about the relevance of this phenomenon
later.}
\end{minipage} }">|; 

$key = q/framebox[0.9textwidth]{partabular{{ll}{tt[{rmitexpr.}]}&--representstheresultoftheexpressioninsidethebracketstabular{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="501" HEIGHT="30" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img27.gif"
 ALT="\framebox[0.9\textwidth]{
\par
\begin{tabular}{ll}
{\tt [{\rm \it expr.}...
...epresents the result of the expression inside the brackets
\end{tabular}
}">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturessladegradation,whereitactsasatagforintracellularproteolysis.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="162" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img3.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...dation, where it acts as a tag for intracellular proteolysis.}
\end{minipage} }">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_ubiquitin_colordisp}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="482" HEIGHT="328" BORDER="0"
 SRC="|."$dir".q|img38.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut2_ubiquitin_colordisp}
}
\end{center}
\end{figure}">|; 

$key = q/leq;MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="15" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img61.gif"
 ALT="$\leq$">|; 

$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_rotations}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="482" HEIGHT="276" BORDER="0"
 SRC="|."$dir".q|img8.gif"
 ALT="\begin{figure}\begin{center}
\includegraphics[scale=0.5]{pictures/tut_rotations}
\end{center}
\end{figure}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6ePSFin{sfFile~{rightarrow{~LoadDataIntoMolecule}.itemize{}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="239" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img44.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...
File&nbsp;$\rightarrow$&nbsp;Load Data Into Molecule}.
\end{itemize} }
\end{minipage} }">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_main_2mols}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="462" HEIGHT="217" BORDER="0"
 SRC="|."$dir".q|img22.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut2_main_2mols}
}
\end{center}
\end{figure}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6slashwww.tcl.tkslashdoc}{http:slashslashwww.tcl.tkslashdocslash}.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="113" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img23.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...ddnormallink{http://www.tcl.tk/doc}{http://www.tcl.tk/doc/}. }
\end{minipage} }">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6ory.Thistrickisbetterthanclickingonthe{sfStart}and{sfEnd}buttons.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="269" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img49.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...ter than clicking on the {\sf
Start} and {\sf End} buttons.}
\end{minipage} }">|; 

$key = q/%latex2htmlidmarker5914framebox[textwidth]{minipage{{.2textwidth}includegraphicsoloringresiduesaccordingtotheirRMSDsimilarlythatinUnitref{unit2}.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="91" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img63.gif"
 ALT="% latex2html id marker 5914
\framebox[\textwidth]{
\begin{minipage}{.2\textwid...
... according to their RMSD similarly that in Unit
\ref{unit2}.}
\end{minipage} }">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6uiuc.eduslashResearchslashvmdslashcurrentslashugslashnode27.html}}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="94" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img10.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...}{http://www.ks.uiuc.edu/Research/vmd/current/ug/node27.html}}
\end{minipage} }">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6,position(x,yandz),charge,mass,occupancyandradius,justtonameafew.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="83" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img30.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...d z), charge, mass, occupancy and radius, just to name a few.}
\end{minipage} }">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut_animate}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="462" HEIGHT="55" BORDER="0"
 SRC="|."$dir".q|img46.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut_animate}
}
\end{center}
\end{figure}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6menu.BesuretheOpenGLdisplaywindowisactivewhenusingtheseshortcuts.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="83" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img54.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...Open GL display window is active when using these shortcuts. }
\end{minipage} }">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslarentpropertiesthatarerelatedtothefunctionalityofthechain.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="131" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img20.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...roperties
that are related to the functionality of the chain.}
\end{minipage} }">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslareundermechanicalstressconfersthemtheirelasticproperties.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="131" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img43.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...der
mechanical stress confers them their elastic properties. }
\end{minipage} }">|; 

$key = q/framebox[0.9textwidth]{partabular{{ll}{ttsource}{itfile}&--runsascriptfromatextfiletabular{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="501" HEIGHT="30" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img35.gif"
 ALT="\framebox[0.9\textwidth]{
\par
\begin{tabular}{ll}
{\tt source} {\it file} &amp; - runs a script from a text file
\end{tabular}
}">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut_bond_dist}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="732" HEIGHT="480" BORDER="0"
 SRC="|."$dir".q|img53.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut_bond_dist}
}
\end{center}
\end{figure}">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_hydrophobicity}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="467" HEIGHT="318" BORDER="0"
 SRC="|."$dir".q|img31.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut2_hydrophobicity}
}
\end{center}
\end{figure}">|; 

$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_unit01_002}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="490" HEIGHT="276" BORDER="0"
 SRC="|."$dir".q|img9.gif"
 ALT="\begin{figure}\begin{center}
\includegraphics[scale=0.5]{pictures/tut_unit01_002}
\end{center}
\end{figure}">|; 

$key = q/{figure}center{htmlimage{scale=0}includegraphics[height=3in]{picturesslashtut0_ubiquitin}center{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="277" HEIGHT="345" BORDER="0"
 SRC="|."$dir".q|img1.gif"
 ALT="\begin{figure}\begin{center}
\includegraphics[height=3in]{pictures/tut0_ubiquitin}
\end{center}\end{figure}">|; 

$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6ouneedtomergebothastructureandacoordinatefileintothesamemolecule.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="126" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img21.gif"
 ALT="\framebox[\textwidth]{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2...
...oth a structure and a coordinate file into the same molecule.}
\end{minipage} }">|; 

$key = q/alpha;MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="13" HEIGHT="13" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img17.gif"
 ALT="$\alpha$">|; 

$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturessladedby58watermolecules,andthathydrogenatomsarenotincluded.}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="557" HEIGHT="131" ALIGN="MIDDLE" BORDER="0"
 SRC="|."$dir".q|img7.gif"
 ALT="\fbox{
\begin{minipage}{.2\textwidth}
\includegraphics[width=2.3 cm, height=2....
...8 water molecules, and
that hydrogen atoms are not included.}
\end{minipage} }">|; 

$key = q/%latex2htmlidmarker5576framebox[textwidth]{minipage{{.2textwidth}includegraphicsytypingthecommand{ttmolssrecalctop}intheTkConsole,whileinframe28.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
 WIDTH="556" HEIGHT="83" ALIGN="BOTTOM" BORDER="0"
 SRC="|."$dir".q|img50.gif"
 ALT="% latex2html id marker 5576
\framebox[\textwidth]{
\begin{minipage}{.2\textwid...
... {\tt mol ssrecalc top} in the Tk Console, while in frame 28.}
\end{minipage} }">|; 

$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_ubiquitin_aligned}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
 WIDTH="480" HEIGHT="306" BORDER="0"
 SRC="|."$dir".q|img34.gif"
 ALT="\begin{figure}\begin{center}
\par
\par
\latex{
\includegraphics[scale=0.5]{pictures/tut2_ubiquitin_aligned}
}
\end{center}
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$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslatolookatsuchanequilibrationtrajectorylaterinthistutorial.}minipage{};MSF=1.6;AAT/;
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$key = q/framebox[0.9textwidth]{partabular{{ll}{ttatomselect}{itmolid}{itselection}&--createsanewatomselectiontabular{};AAT/;
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{\tt atomselect} {\it molid} {\it selection} &amp; - creates a new atom selection
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$key = q/fbox{minipage{[c]{textwidth}centering{noindentsmall{smallAcurrentversionofthistuashslashwww.ks.uiuc.eduslashTrainingslashTutorialsslash}}}minipage{};MSF=1.6;AAT/;
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$key = q/rightarrow;MSF=1.6;AAT/;
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$key = q/framebox[0.9textwidth]{partabular{{ll}{ttmeasurefit}{itatomsel1}{itatomsel2}&--calculatesthebestfitmatrixtabular{};AAT/;
$cached_env_img{$key} = q|<IMG
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{\tt measure fit} {\i...
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$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_unit01_008}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
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$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6intheX11environment.MakesureX11isrunninginorderforxmgracetostart.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
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...nt. Make sure X11 is running in order for xmgrace to
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$key = q/fbox{minipage{{.2textwidth}includegraphics[width=2.3cm,height=2.3cm]{picturesslaump.Youwillhaveidentifiedkeyfeaturesofubiquitinunfolding!}minipage{};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
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...You will have identified key features of ubiquitin unfolding!}
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$key = q/};MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
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$key = q/framebox[0.9textwidth]{partabular{{ll}{ttset}{itvariable}{itvalue}&--setsthevalule}{ttputs}{ttdollar}{itvariable}&--printsoutthevalueof{itvariable}tabular{};AAT/;
$cached_env_img{$key} = q|<IMG
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{\tt set} {\it variab...
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$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_unit01_004}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
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$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_colorrange}}center{{{{figure};FSF=1.6;AAF/;
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$key = q/beta;MSF=1.6;AAT/;
$cached_env_img{$key} = q|<IMG
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$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut_traj_nice}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
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\latex{
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$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut_bond_plot}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
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\latex{
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$key = q/framebox[textwidth]{minipage{{.2textwidth}includegraphics[width=2.5cm,height=1.6r}windowandpressthe{sfLoad}button.VMDwilldownloaditautomatically.}minipage{};AAT/;
$cached_env_img{$key} = q|<IMG
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...s the {\sf Load} button.
VMD will download it automatically.}
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$key = q/{figure}center{{par{htmlimage{scale=2.0}{par{latex{includegraphics[scale=0.5]{picturesslashtut2_colorscale}}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
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$key = q/{figure}center{htmlimage{scale=2.0}includegraphics[scale=0.5]{picturesslashtut_unit01_005}center{{{{figure};FSF=1.6;AAF/;
$cached_env_img{$key} = q|<IMG
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1;

