| version 1.9 | version 1.10 |
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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: 1.9 $ $Date: 2002/10/18 16:31:05 $ | % $Revision: 1.10 $ $Date: 2002/10/28 21:35:13 $ |
| % | % |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| % DESCRIPTION: | % DESCRIPTION: |
| |
| \chapter{Molecular Drawing Methods} | \chapter{Molecular Drawing Methods} |
| \label{ug:topic:drawing} | \label{ug:topic:drawing} |
| | |
| \section {Molecular Drawing Methods} | \section {Representations} |
| JMV allows you to view the molecule with different representations. To change the representation, select ``Representation'' from the ``View'' menu, and select one of the choices. | JMV allows you to view the molecule with different representations. To change the representation, select ``Representation'' from the ``View'' menu, and select one of the choices. |
| %%Please note that these changes are only applicable to PDB files, and will not affect VRML files. The current representations available are: | %%Please note that these changes are only applicable to PDB files, and will not affect VRML files. The current representations available are: |
| | |
| \subsection{Lines} | \subsection{Lines} |
| \index{lines representation} | \begin{rawhtml} |
| 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. | <CENTER> |
| | \end{rawhtml} |
| | \myfigurepage{Alanin-Lines.eps}{Lines in JMV}{fig:ug:Lines} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| | 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}) |
| | |
| \subsection{VDW} | |
| \index{VDW representation} | |
| ``VDW'' draws the atoms as spheres. Each sphere is drawn with a radius that depends on the atom's radius. | |
| | |
| \subsection{Bonds} | \subsection{Bonds} |
| | \begin{rawhtml} |
| | <CENTER> |
| | \end{rawhtml} |
| | \myfigurepage{Alanin-Bonds.eps}{Bonds in JMV}{fig:ug:Bonds} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| \index{bonds!representation} | \index{bonds!representation} |
| 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. | 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}) |
| | |
| | \subsection{VDW} |
| | \begin{rawhtml} |
| | <CENTER> |
| | \end{rawhtml} |
| | \myfigurepage{Alanin-VDW.eps}{VDW in JMV}{fig:ug:VDW} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| | \index{VDW representation} |
| | ``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}) |
| | |
| \subsection{CPK} | \subsection{CPK} |
| | \begin{rawhtml} |
| | <CENTER> |
| | \end{rawhtml} |
| | \myfigurepage{Alanin-CPK.eps}{CPK in JMV}{fig:ug:CPK} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| \index{CPK representation} | \index{CPK representation} |
| ``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. | ``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}) |
| | |
| | \subsection{Licorice} |
| | \begin{rawhtml} |
| | <CENTER> |
| | \end{rawhtml} |
| | \myfigurepage{Alanin-Licorice.eps}{Licorice in JMV}{fig:ug:Licorice} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| | \index{licorice representation} |
| | ``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}) |
| | |
| \subsection{Trace} | \subsection{Trace} |
| | \begin{rawhtml} |
| | <CENTER> |
| | \end{rawhtml} |
| | \myfigurepage{Alanin-Trace.eps}{Trace in JMV}{fig:ug:Trace} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| \index{trace representation} | \index{trace representation} |
| ``Trace'' draws cylinders connecting the ``Carbon-alpha'' (CA) atoms in the molecule. | ``Trace'' draws cylinders connecting the ``Carbon-alpha'' (CA) atoms in the molecule. (See Fig. \ref{fig:ug:Trace}) |
| | |
| \subsection{Tube} | \subsection{Tube} |
| | \begin{rawhtml} |
| | <CENTER> |
| | \end{rawhtml} |
| | \myfigure{Alanin-Tube.eps}{Tube in JMV}{fig:ug:Tube} |
| | \begin{rawhtml} |
| | </CENTER> |
| | \end{rawhtml} |
| \index{tube representation} | \index{tube representation} |
| ``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. | ``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}) |
| | |
| \subsection{Licorice} | |
| \index{licorice representation} | |
| ``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. | |