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Coloring Atoms Using Maestro Commands |
Maestro commands can be used to apply atom colors, by typing them in the Commands text box in the main window (Command Input Area). To apply atom colors, you can use one of the following commands:
coloratomrgb red=int green=int blue=int
ASL-expression
coloratom { color=colorname | cindex=colorindx }
ASL-expression/
You can specify the color as an RGB color with integers from 0 to 255 for each of the color components in the first command, or you can use a color palette of 256 colors, which are represented either by an index or a name in the second command.
Examples:
To color atom 22 red: coloratomrgb red=255 green=0 blue=0 atom. 22
To color residue 14 green: coloratom color=green res. 14
To color residue 14 with the color at color index 5:
coloratom cindex=5 res. 14
To apply a color scheme to atoms, use the command:
colorscheme scheme=scheme-name asl-expression
where scheme-name is the short name listed in the scheme.res resource file. These names are given below with the long name as it appears in Maestro.
| bfactor | Atom PDB B Factor (Temperature Factor) |
| acharge | Atom Partial Charge |
| mmatype | Atom Type (MacroModel) |
| chain | Chain Name |
| densityfit | Density Fit |
| element | Element |
| element_light_carbons | Element (Light Carbons) |
| element_customc_black | Element (Black Carbons) |
| element_customc_gray | Element (Gray Carbons) |
| element_customc_darkblue | Element (Dark Blue Carbons) |
| element_customc_blue | Element (Blue Carbons) |
| element_customc_aquamarine | Element (Aquamarine Carbons) |
| element_customc_turquoise | Element (Turquoise Carbons) |
| element_customc_springgreen_carbons | Element (Spring Green Carbons) |
| element_customc_darkgreen | Element (Dark Green Carbons) |
| element_customc_green | Element (Green Carbons) |
| element_customc_limegreen | Element (Lime Green Carbons) |
| element_customc_yellowgreen | Element (Yellow Green Carbons) |
| element_customc_yellow | Element (Yellow Carbons) |
| element_customc_orange | Element (Orange Carbons) |
| element_customc_maroon | Element (Maroon Carbons) |
| element_customc_red | Element (Red Carbons) |
| element_customc_pink | Element (Pink Carbons) |
| element_customc_plum | Element (Plum Carbons) |
| element_customc_purple | Element (Purple Carbons) |
| element_customc_bluepurple | Element (Blue Purple Carbons) |
| element_customc_white | Element (White Carbons) |
| element_customl_black | Element (Black Ligand) |
| element_customl_gray | Element (Gray Ligand) |
| element_customl_darkblue | Element (Dark Blue Ligand) |
| element_customl_blue | Element (Blue Ligand) |
| element_customl_aquamarine | Element (Aquamarine Ligand) |
| element_customl_turquoise | Element (Turquoise Ligand) |
| element_customl_springgreen_carbons | Element (Spring Green Ligand) |
| element_customl_darkgreen | Element (Dark Green Ligand) |
| element_customl_green | Element (Green Ligand) |
| element_customl_limegreen | Element (Lime Green Ligand) |
| element_customl_yellowgreen | Element (Yellow Green Ligand) |
| element_customl_yellow | Element (Yellow Ligand) |
| element_customl_orange | Element (Orange Ligand) |
| element_customl_maroon | Element (Maroon Ligand) |
| element_customl_red | Element (Red Ligand) |
| element_customl_pink | Element (Pink Ligand) |
| element_customl_plum | Element (Plum Ligand) |
| element_customl_purple | Element (Purple Ligand) |
| element_customl_bluepurple | Element (Blue Purple Ligand) |
| element_customl_white | Element (White Ligand) |
| entrycarbon | Element (Entry Carbons) |
| element_chain | Element (Chain Name Carbons) |
| clmolcarbon | Element (Molecule Number Carbons) |
| entry | Entry |
| reshyd_litangwingreen | Hydrophobicity - Li-Tang-Wingreen |
| reshyd_kytedoolittle | Hydrophobicity - Kyte-Doolittle |
| reshyd_blackmould | Hydrophobicity - Black-Mould |
| clmol | Molecule Number |
| clmolsize | Molecule Size |
| pdbconversion | PDB Conversion Status |
| reschg | Residue Charge |
| resprop | Residue Property |
| respos | Residue Position |
| restype | Residue Type |
| spectrumrestype | Residue Type (spectrum) |
| secstruct | Secondary Structure |
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