Customizing Color Scheme Files
Each of the standard color schemes is defined in a separate file in the mmlibs/schemes subdirectory of the installation resources directory. By convention, color scheme files have the extension .sch. The schemes are called by Maestro using the file scheme.res, which is in the installation resources directory. You can customize color schemes from Maestro in the Color Schemes settings section of the Preferences Panel. If you want to edit the files directly, or create an entire set of custom color schemes, you can do so as follows.
To define your own color schemes:
-
Create a
scheme.resfile in your Maestro user resources directory, or copyscheme.resfrom the installation resources directory and edit it. -
Create a
schemessubdirectory in your Maestro user resources directory. -
Create color scheme files
scheme.schin theschemessubdirectory, or copy the.schfiles from theschemessubdirectory of the installation resources directory and edit them.
The scheme.res file contains a three-line description of each scheme. The three lines contain:
- The short name of the color scheme, used in the
colorschemecommand - The display name of the color scheme, used in Maestro menus and lists
- The name of the file in the
schemessubdirectory that contains the scheme definition
Comments can be included in this file by putting a "#" at the beginning of each line that contains a comment (the "#" must be in the first column). The short names and the display names of the standard color schemes are listed below.
| Aliases | ASL Expression |
|---|---|
| intersection, INTERSECTION, & | and |
| UNION, union, | | or |
| ! | not |
| MOL, mol | mol. |
| ATOM, atom | atom. |
| RES, res | res. |
| CHAIN, chain | chain. |
| backbone, BACKBONE | ((res.pt ACE) OR (atom.pt ca,c,n,o,oxt OR (a.e H and withinbonds 1 atom.pt ca, n)) and not (res.pt hoh or res.pt spc or res.pt t4p or res.pt t3p or res.pt t5p or res.pt t4pe or res.pt t4pd or res.pt spce or res.pt t4p5 or res.pt DPPC, POPC, POPE, DMPC, DOPC, DOPS, POPS, DPPS, DMPS, DPPE, DMPE, DOPE, PIP, POPA, DOPA, DMPA, DPPA or (res.pt GLY AND atom.pt 2HA, HA3))) |
| SIDECHAIN, sidechain | ((atom.pt 3HE, 1HG, OD1, OD2, HB, HE, HG, HH, 3HD1, 3HD2, 2HG1, 1HZ, 2HG2, HZ2, HZ3, 3HZ, CE1, CE2, CE3, HG1, HZ, OE1, OE2, 2HD1, 2HD2, 1HG1, 1HG2, 2HH1, 2HH2, 2HB, HD1, HD2, 2HD, 2HE, 2HG, HH2, ND1, ND2, NH1, NH2, 1HD1, CZ2, CZ3, 2HE2, 1HH1, NE, 1HH2, 2HZ, CG1, CG2, HE1, HE2, HE3, NE1, CB, NE2, OG1, CD, CE, NZ, CG, 1HE2, 3HG1, 3HG2, OG, OH, SD, CD1, CD2, SG, 1HB, CH2, 1HD, 3HB, CZ, 1HE, 1HD2, HH1, HE3, HD13, HD23, HG12, HZ1, HG21, HD12, HD22, HG11, HH12, HH22, HB2, HG2, HD11, HE22, HH11, HH21, HE21, HG13, HG23, HB3, HD21, HG3, HB1, HG22, HD3 ) or ( res.pt MSE & atom.pt "SE ") or ( res.pt gly & atom.pt 2ha,ha3 ) and not (res.pt gly & atom.pt 1ha,ha2 ) and not ( res.pt DPPC, POPC, POPE, DMPC, DOPC, DOPS, POPS, DPPS, DMPS, DPPE, DMPE, DOPE, PIP, POPA, DOPA, DMPA, DPPA) ) |
| WATER, water | (/H2-O3-H2/ or atom.mtype OW or res.pt hoh, spc, t4p, t3p, t5p, t4pe, t4pd, spce, t4p5, dod) |
| SOLVENT, solvent | (/H2-O3-H2/ or atom.mtype OW or res.pt hoh, spc, t4p, t3p, t5p, t4pe, t4pd, spce, t4p5, dod or res.pt GOL, EDO, DMS, PEG, MPD, PG4, BME, PGE, IPA, 1PE, EOH, P6G, DMF, MOH, POL, 2PE, PE4, ETA, 15P, 12P, P33, PE5, TBU, CCN, CXE, 7PE, NME, PE3, PE6, ACN, P4C, PE8, NEH, XPE, 1BO, N8E, DMN, CE1, PYE, C10, SBT, MB3) |
| IONS, ions | (fillmol ( atom.formalcharge <0 or atom.formalcharge > 0 ) and (mol.atoms < 10 ) ) |
| MEMBRANE, membrane | ( res. POP, POPE, POPC, DPPC, DMPC ) |
| protein, PROTEIN | (fillres at.pt " CA " or res.pt ACE) |
| workspace_selection | atom.selected |
| displayed_atoms, DISPLAYED_ATOMS | atom.disp |
| protein_near_ligand, PROTEIN_NEAR_LIGAND | fillres( (fillres at.pt " CA " or res.pt ACE) and within 5.0 ligand ) |
| all_hydrogens, ALL_HYDROGENS | atom.ele H |
| non_polar_hydrogens, NON_POLAR_HYDROGENS | (atom.ele H and /C0-H0/) |
| non_polar_ligand_hydrogens, NON_POLAR_LIGAND_HYDROGENS | (atom.ele H and /C0-H0/ and ligand) |
| polar_hydrogens, POLAR_HYDROGENS | (atom.ele H and not /C0-H0/) |
| heavy_atoms, HEAVY_ATOMS | not atom.ele H |
| METALLOIDS, metalloids | atom.atomicnum 5,14,32,33,51,52,84,85 |
| METALS, metals | atom.atomicnum 3,4,11-13,19-31,37-50,55-83,87-109 |
| NUCLEIC_ACIDS, nucleic_acids | (res. " DA "," DC "," DG "," DT "," C "," U "," G "," A ") |
| receptor, RECEPTOR | ( ( (fillres at.pt " CA " or res.pt ACE) or (res. " DA "," DC "," DG "," DT "," C "," U "," G "," A ") ) and ( not ligand )) |
| DNA, dna | (res. " DA "," DC "," DG "," DT ") |
| RNA, rna | (res. " C "," U "," G "," A ") |
| NUCLEIC_BACKBONE, nucleic_backbone | (res. " DA " " DC " " DG " " DT " " C " " U " " G " " A " AND NOT atom.pt N9 N1 AND withinbonds 1 atom.pt " C3'" " O3'" " O5'" P " C4'" " C5'" " O4'" " C1'" " C2'" " O2'") |
| NUCLEIC_SIDECHAIN, nucleic_sidechain | (res. " DA " " DC " " DG " " DT " " C " " U " " G " " A " AND NOT atom.pt " C1'" AND withinbonds 1 atom.pt N1 C2 N2 O2 N3 C4 N4 O4 C5 C6 N6 O6 C7 N7 C8 N9) |
You can add color schemes for general use by editing the files that define Maestro's standard schemes. There are some restrictions: the "element_custom" schemes cannot be edited or copied, as the color is dymamically chosen, and the schemes are keyed off a single color scheme (.sch) file rather than separate files. These schemes are enclosed in square brackets in scheme.res under the parent schemes, element_customC and element_customL.
The color scheme files contain a number of rules, one rule per line, which are applied in the order they appear in the file. Each rule consists of the name of a color as it appears in the colors.res file in the installation resources directory or the 6-digit hexadecimal RGB code for the color; an ASL specification that describes which atoms are to have that color, and an optional description. Color names must be a single token; if the color names have an embedded space, they must be quoted (for example: "spring green"). At the end of the file, you can add a description of the color scheme by adding a line with the word DESCRIPTION and following it with any number of lines that contain the description.
Here is an example of a possible color scheme:
white atom.ele * blue atom.ele N red atom.ele O
This scheme first sets all atoms to white, then colors all the nitrogen atoms blue and the oxygen atoms red. Any number of such rules can be included in color scheme files.