| version 1.11 | version 1.12 |
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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: 1.11 $ $Date: 2002/10/28 21:35:13 $ | % $Revision: 1.12 $ $Date: 2002/10/28 23:32:29 $ |
| % | % |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| % DESCRIPTION: | % DESCRIPTION: |
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| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| \section{Molecule Coloring Schemes} | \section{Molecule Coloring Schemes} |
| \index{coloring!methods} | \index{coloring methods} |
| | |
| \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: |
| |
| Phosphorus: Tan\newline | Phosphorus: Tan\newline |
| Zinc: Silver\newline | Zinc: Silver\newline |
| Other: Green | Other: Green |
| | \index{color schemes!Name} |
| | \index{Name color scheme} |
| | |
| \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. | \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. |
| | \index{color schemes!Index} |
| | \index{Index color scheme} |
| | |
| \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. | \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. |
| | \index{color schemes!Residue Name} |
| | \index{Residue Name color scheme} |
| | |
| \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. | \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. |
| | \index{color schemes!Chain} |
| | \index{Chain color scheme} |
| | |
| \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. | \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. |
| | \index{color schemes!Segment} |
| | \index{Segment color scheme} |
| | |
| \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:\\ | \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 | Sheet: Blue |
| | \index{color schemes!Structure} |
| | \index{Structure color scheme} |