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Atom Color Schemes |
An atom color scheme is a set of rules that describes how atoms are to be colored. Maestro supplies a set of standard schemes (described below), which you can apply and customize, and you can add your own color schemes, by using the Color Schemes panel, or by editing resource files (see Customizing Color Schemes by Editing Resource Files).
There are three ways of applying a color scheme:
Use the Color Scheme button on the Representation toolbar to apply a color scheme to all atoms.
Use the Atom and Bond Coloring panel (Workspace menu) to apply a color scheme to selected atoms.
Use a Maestro command (see Coloring Atoms Using Maestro Commands for details).
Applies a spectrum of colors to atoms depending on the PDB temperature factor (B factor).
Applies a spectrum of colors to denote sign and magnitude of charge.
Colors each atom according to the MacroModel atom type.
Colors each chain with a unique color corresponding to its single-letter name.
Colors atoms according to the value of the PrimeX density fit.
Gives each atom a color according to its atomic number. Light elements continue to have their standard Maestro colors, as in the Atom Type scheme. Other elements are divided into several groups, and each group has a unique color. For example, the first row of transition metals is turquoise. In this color scheme, atoms of the same element are always the same color, regardless of their formal charge or MacroModel atom type. This is the default coloring scheme.
Colors each atom according to its atomic number, as in the Element scheme, except that carbon atoms are light gray, and hydrogens are cyan.
Colors each atom according to its atomic number, as in the Element scheme, except that carbon atoms are colored with a custom color. The schemes for each custom color are listed below this heading.
Colors each atom according to its atomic number, as in the Element scheme, except that carbon atoms in the ligand are colored with a custom color. The schemes for each custom color are listed below this heading.
Colors all atoms except carbon atoms according to the atomic number, as in the Element scheme, and colors carbon atoms by entry number, cycling through a list of 12 colors.
Colors carbon atoms by chain name, using 26 colors for names A–Z and repeating for names 1–26, and colors other atoms by Element.
Colors carbon atoms by molecule number, cycling through a list of 12 colors, and colors other atoms by Element.
Colors atoms according to the entry to which they belong. The scheme cycles through a list of 12 colors, applying them in turn to the entries in the Workspace, in the order in which they appear in the Project Table.
Colors atoms according to the entry ID of the entry to which they belong. The scheme uses a list of 12 colors, applying them by the value of the entry ID, modulo 12: thus, each entry whose remainder when the entry ID is divided by 12 has the same color.
Three schemes for hydrophobicity are available: Li-Tang-Wingreen (Phys. Rev. Lett. 1997, 79, 765), Kyte-Doolittle (J. Mol. Biol 1982 157, 105), and Black-Mould (Anal. Biochem. 1991, 193, 72). All three schemes rely on the residue name to determine the appropriate property value for the color scheme.
Colors each molecule by number. The scheme cycles through a list of 12 colors.
Colors atoms by molecule size, making it easier to locate ligands in a structure.
Colors residues in structures imported from the PDB by the status of their conversion:
| Gray | Standard residues, no conversion problems |
| Green | Residue with alternate location indicator |
| Blue | Standard residue with unknown atom names |
| Red | Standard residue with missing atoms |
| Orange | Non-standard residue, bond orders may need correcting |
Colors amino acid residues according to charge. Positive charges are blue, negative charges are red.
Colors amino acid residues according to hydrophobicity, charge, and polarity.
| Gray | GLY and atoms without PDB residue names |
| Dark green | Hydrophobic ( ALA, CYS, ILE, LEU, MET, PHE, TRP, TYR, VAL, PRO ) |
| Cyan | Polar uncharged (SER, THR, HIS, HIE, GLN, GLH, LYN, ASN, ASH) |
| Blue | Positives ( LYS, ARG, HIP ) |
| Red | Negatives ( ASP, GLU ) |
| Purple | Purine ( G, A, I ) |
| Sienna | Pyrimidine ( C, T, U ) |
Colors amino acid residues by residue number. The first 10% (including the N-terminus) of the residues in a chain are dark blue, the last 10% (C-terminus) are red and there is a color ramp between those ends.
Colors amino acid residues by residue type.
Colors amino acid residues by residue type, with finer distinctions between conservatively mutated and conserved residues.
Colors residues according to protein secondary structure (strand, loop, helix). To assign secondary structure, choose Assign Secondary Structure from the Tools menu.
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