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| % | % |
| % $RCSfile: ug_mol_reps.tex,v $ | % $RCSfile: ug_mol_reps.tex,v $ |
| % $Author: mbach $ $Locker: $ $State: Exp $ | % $Author: mbach $ $Locker: $ $State: Exp $ |
| % $Revision: 1.10 $ $Date: 2002/10/28 21:35:13 $ | % $Revision: 1.11 $ $Date: 2002/10/28 23:32:29 $ |
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| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| % DESCRIPTION: | % DESCRIPTION: |
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| \begin{rawhtml} | \begin{rawhtml} |
| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| | \index{Lines representation} |
| | \index{Representations!Lines} |
| The simplest representation is `Lines', which is also known as `wireframe'. It draws a line between each atom and the atoms to which it is bonded. The first half of each bond is colored appropriately for the first atom, while the color of the final half corresponds to the second atom. (See Fig. \ref{fig:ug:Lines}) | The simplest representation is `Lines', which is also known as `wireframe'. It draws a line between each atom and the atoms to which it is bonded. The first half of each bond is colored appropriately for the first atom, while the color of the final half corresponds to the second atom. (See Fig. \ref{fig:ug:Lines}) |
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| \subsection{Bonds} | \subsection{Bonds} |
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| \begin{rawhtml} | \begin{rawhtml} |
| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| \index{bonds!representation} | \index{Bonds representation} |
| | \index{Representations!Bonds} |
| Nearly everything about this option is the same as ``Lines'' except that instead of drawing a bond as a line between two atoms, it is drawn as a cylinder. (See Fig. \ref{fig:ug:Bonds}) | Nearly everything about this option is the same as ``Lines'' except that instead of drawing a bond as a line between two atoms, it is drawn as a cylinder. (See Fig. \ref{fig:ug:Bonds}) |
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| \subsection{VDW} | \subsection{VDW} |
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| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| \index{VDW representation} | \index{VDW representation} |
| | \index{Representations!VDW} |
| ``VDW'' draws the atoms as spheres. Each sphere is drawn with a radius that depends on the atom's radius. (See Fig. \ref{fig:ug:VDW}) | ``VDW'' draws the atoms as spheres. Each sphere is drawn with a radius that depends on the atom's radius. (See Fig. \ref{fig:ug:VDW}) |
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| \subsection{CPK} | \subsection{CPK} |
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| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| \index{CPK representation} | \index{CPK representation} |
| | \index{Representations!CPK} |
| ``CPK'' is a combination of ``Bonds'' and ``VDW'' in that it draws the atoms as spheres and also draws the bonds connecting them. The sphere are drawn much smaller than in VDW, and the cylinders are thinner than in Bonds. Each sphere is drawn with a radius that depends on the atom type. (See Fig. \ref{fig:ug:CPK}) | ``CPK'' is a combination of ``Bonds'' and ``VDW'' in that it draws the atoms as spheres and also draws the bonds connecting them. The sphere are drawn much smaller than in VDW, and the cylinders are thinner than in Bonds. Each sphere is drawn with a radius that depends on the atom type. (See Fig. \ref{fig:ug:CPK}) |
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| \subsection{Licorice} | \subsection{Licorice} |
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| \begin{rawhtml} | \begin{rawhtml} |
| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| \index{licorice representation} | \index{Licorice representation} |
| | \index{Representations!Licorice} |
| ``Licorice'' draws the atoms as spheres and the bonds as cylinders. The difference between this and `CPK' is that the sphere radii and cylinder diamoneters are the same. (See Fig. \ref{fig:ug:Licorice}) | ``Licorice'' draws the atoms as spheres and the bonds as cylinders. The difference between this and `CPK' is that the sphere radii and cylinder diamoneters are the same. (See Fig. \ref{fig:ug:Licorice}) |
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| \subsection{Trace} | \subsection{Trace} |
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| \begin{rawhtml} | \begin{rawhtml} |
| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| \index{trace representation} | \index{Trace representation} |
| | \index{Representations!Trace} |
| ``Trace'' draws cylinders connecting the ``Carbon-alpha'' (CA) atoms in the molecule. (See Fig. \ref{fig:ug:Trace}) | ``Trace'' draws cylinders connecting the ``Carbon-alpha'' (CA) atoms in the molecule. (See Fig. \ref{fig:ug:Trace}) |
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| \subsection{Tube} | \subsection{Tube} |
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| \begin{rawhtml} | \begin{rawhtml} |
| </CENTER> | </CENTER> |
| \end{rawhtml} | \end{rawhtml} |
| \index{tube representation} | \index{Tube representation} |
| | \index{Representations!Tube} |
| ``Tube'' draws a spline curve that goes through all the ``Carbon-alpha'' (CA) atoms in the molecule. The spline curve is drawn as a series of cylinders. This is similar to Tube, except the atoms are directly connected by a smooth spline, not just straight cylinders. (See Fig. \ref{fig:ug:Tube}) | ``Tube'' draws a spline curve that goes through all the ``Carbon-alpha'' (CA) atoms in the molecule. The spline curve is drawn as a series of cylinders. This is similar to Tube, except the atoms are directly connected by a smooth spline, not just straight cylinders. (See Fig. \ref{fig:ug:Tube}) |
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