Maestro User Manual

Chapter 7: Changing the Appearance of Structures

Schrödinger Software Release 2015-2 

136

Table 7.1. Standard color schemes

Scheme

Description

Atom PDB B Factor 

(Temperature Factor) 

Apply a spectrum of colors to atoms depending on the PDB temperature 

factor (B factor).

Atom Partial Charge

Apply a spectrum of colors to denote sign and magnitude of charge. 

Atom Type (MacroModel)

Colors each atom type by the older MacroModel coloring scheme. 

Chain Name

Color each chain with a unique color corresponding to its single-letter 

name. 

Density Fit

Color atoms according to the value of the PrimeX density fit. 

Element

Color atoms according to their 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.

Element (Light Carbons)

Color atoms according to their atomic number, as in the Element scheme, 

except that carbon atoms are light gray, and hydrogens are cyan. 

Element (

color

 Carbons)

Color atoms according to their atomic number, as in the Element scheme, 

except that carbon atoms are colored with the stated color. These schemes 

appear under the heading 

Element (Custom Carbons)

.

Element (

color

 Ligand)

Color atoms according to their atomic number, as in the Element scheme, 

except that atoms in the ligand are colored with the stated color. These 

schemes appear under the heading 

Element (Custom Ligand)

.

Element (Entry Carbons)

Color all atoms except carbon atoms according to their atomic number, as 

in the Element scheme, and colors carbon atoms by entry number, cycling 

through a list of 12 colors. 

Element (Chain Name 

Carbons)

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. 

Element (Molecule 

Number Carbons)

Colors carbon atoms by molecule number, cycling through a list of 12 

colors, and colors other atoms by Element. 

Entry

Colors atoms according to the entry to which they belong. The scheme 

cycles through a list of 12 colors. 

Entry ID

 

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. 

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Chapter 7: Changing the Appearance of Structures

Maestro 10.2 User Manual

137

Hydrophobicity

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. 

Molecule Number

Color each molecule by number. The scheme cycles through a list of 12 

colors. 

Molecule Size

Color atoms by molecule size, making it easier to locate ligands in a 

structure. 

PDB Conversion Status

Color residues in structures imported from the PDB by the status of their 

conversion:

Gray   

Standard residues, no conversion problems

Green  

Residue with alternate position indicator

Blue   

Standard residue with unknown atom names

Cyan

Residue adjacent to gap

Red  

Standard 

residue with missing atoms

Orange  

Non-standard residue, bond orders may need correcting

Residue Charge

Color amino acid residues according to charge. Positive charges are blue, 

negative charges are red.

Residue Property

Color amino acid residues according to hydrophobicity, charge, and 

polarity.

gray

GLY and atoms without PDB residue names

dark green Hydrophobic residues: ALA, CYS, ILE, LEU, MET, PHE, 

TRP, TYR, VAL, PRO   

cyan

Polar uncharged: SER, THR, HIS, GLN, ASN

blue

Positively charged: LYS, ARG 

red

Negatively charged ASP, GLU 

purple

Purines: G, A, I 

sienna

Pyrimidines: C, T, U 

Residue Position

Color 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. 

Residue Type

Color amino acid residues by residue type. 

Residue Type (spectrum)

Color amino acid residues by residue type, with finer distinctions 

between conservatively mutated and conserved residues. 

Secondary Structure

Color residues according to protein secondary structure (strand, loop, 

helix). To assign secondary structure, choose Assign Secondary Structure 

from the Tools menu. 

Table 7.1. Standard color schemes (Continued)

Scheme

Description

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