| version 1.9 | version 1.10 |
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| % | % |
| % $RCSfile: ug_mol_colors.tex,v $ | % $RCSfile: ug_mol_colors.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: 2002/10/25 16:59:26 $ |
| % | % |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| % DESCRIPTION: | % DESCRIPTION: |
| |
| % Describes the coloring schemes available in JMV | % Describes the coloring schemes available in JMV |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| \chapter{Molecule Coloring Schemes} | \section{Molecule Coloring Schemes} |
| \label{ug:topic:coloring} | |
| \index{coloring!methods} | \index{coloring!methods} |
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| \JMV\ implements a variety of ways to color the molecule. To change the coloring method, select ``Color by'' from the ``View menu'', and select one of the choices. | \JMV\ implements a variety of ways to color the molecule. To change the coloring method, select ``Color by'' 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 choices are: | %% Please note that these changes are only applicable to PDB files, and will not affect VRML files. The choices are: |
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| \begin{table}[htb] | \subsection{Name} Each atom type is assigned a different color. These colors are:\\ |
| \hspace{.1in} | |
| \begin{tabular}{|l|p{6in}|} \hline | |
| {\em Style} & {\em Description} \\ \hline | |
| Name & Each atom type is assigned a different color. These colors are: | |
| | |
| Carbon: Cyan\newline | Carbon: Cyan\newline |
| Hydrogen: White\newline | Hydrogen: White\newline |
| |
| Sulfur: Yellow\newline | Sulfur: Yellow\newline |
| Phosphorus: Tan\newline | Phosphorus: Tan\newline |
| Zinc: Silver\newline | Zinc: Silver\newline |
| Other: Green\\ \hline | Other: Green\\ |
| | |
| Index & The PDB file assigns each atom a unique index identifier. In the Index color scheme, \JMV\ creates a color gradient that creates a smooth color transition going through each atom, in order of their index numbers.\\ \hline | \subsection{Index} The PDB file assigns each atom a unique index identifier. In the Index color scheme, \JMV\ creates a color gradient that creates a smooth color transition going through each atom, in order of their index numbers. |
| | |
| Resname & In the PDB file, each atom belongs to a certain residue.The Resname color scheme assigns a color to each residue name (based on the gradient), and colors each residue with the given color.\\ \hline | \subsection{Resname}In the PDB file, each atom belongs to a certain residue.The Resname color scheme assigns a color to each residue name (based on the gradient), and colors each residue with the given color. |
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| Chain & In the PDB file, each atom belongs to a certain chain. The Chain color scheme assigns a color to each chain (based on the gradient), and colors each chain with the given color.\\ \hline | \subsection{Chain}In the PDB file, each atom belongs to a certain chain. The Chain color scheme assigns a color to each chain (based on the gradient), and colors each chain with the given color. |
| | |
| Segment & In the PDB file, each atom belongs to a certain segment. The Segment color scheme assigns a color to each segment (based on the gradient), and colors each segment with the given color.\\ \hline | \subsection{Segment}In the PDB file, each atom belongs to a certain segment. The Segment color scheme assigns a color to each segment (based on the gradient), and colors each segment with the given color. |
| | |
| Structure & Certain series of atoms may have a ``structure'' associated with them. If these structures are written in the PDB file, \JMV\ can color the molecule by structure. The structures and their corresponding colors are:\newline | \subsection{Structure}Certain series of atoms may have a ``structure'' associated with them. If these structures are written in the PDB file, \JMV\ can color the molecule by structure. The structures and their corresponding colors are: |
| | |
| No structure specified: White\newline | No structure specified: White\newline |
| Helix: Red\newline | Helix: Red\newline |
| Turn: Green\newline | Turn: Green\newline |
| Sheet: Blue\newline | Sheet: Blue\newline |
| \\ | |
| \hline | |
| | |
| \end{tabular} | |
| \end{table} | |