Color Schemes

atom color

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. You can customize color schemes and add your own color schemes in the Color by Atom Property Dialog Box, the Color Schemes section of the Preferences Panel, or by editing resource files (see Customizing Color Scheme Files).

Atom PDB B Factor (Temperature Factor)

Applies a spectrum of colors to atoms depending on the PDB temperature factor (B factor).

Atom Partial Charge

Applies a spectrum of colors to denote sign and magnitude of charge, in 8 steps.

Atom Partial Charge (new)

Applies a spectrum of colors to denote sign and magnitude of charge, in 66 steps.

Atom Type (MacroModel)

Colors each atom according to the MacroModel atom type.

Chain

Colors each chain with a different color.

Chain Name

Colors each chain according to its name. Chains with the same name have the same color; chains with different names have different colors.

Density Fit

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

Element

Gives each atom a color according to its atomic number. In this color scheme, atoms of the same element are always the same color, regardless of their formal charge or atom type.

H

                               

He

Li

Be

                   

B

C

N

O

F

Ne

Na

Mg

                   

Al

Si

P

S

Cl

Ar

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr

Rb

Sr

Y

Zr

Nb

Mo

Tc

Ru

Rh

Pd

Ag

Cd

In

Sn

Sb

Te

I

Xe

Cs

Ba

 

Hf

Ta

W

Re

Os

Ir

Pt

Au

Hg

Tl

Pb

Bi

Po

At

Rn

Fr

Ra

 

Rf

Db

Sg

Bh

Hs

Mt

Ds

Rg

Cn

Nh

Fl

Mc

Lv

Ts

Og

                                   
   

La

Ce

Pr

Nd

Pm

Sm

Eu

Gd

Tb

Dy

Ho

Er

Tm

Yb

Lu

 
   

Ac

Th

Pa

U

Np

Pu

Am

Cm

Bk

Cf

Es

Fm

Md

No

Lr

 
Element (Light Carbons)

Colors each atom according to its atomic number, as in the Element scheme, except that carbon atoms are light gray, and hydrogens are cyan (the Sybyl element color scheme).

Element (Custom Carbons)

Colors each atom according to its atomic number, as in the Element scheme, and lets you dynamically choose a color for the carbon atoms.

Element (Custom Ligand)

Colors each atom according to its atomic number, as in the Element scheme, and lets you dynamically choose a color for the ligand carbon atoms.

Element (Entry Carbons)

Colors all atoms except carbon atoms according to the atomic number, as in the Element scheme, and colors carbon atoms by order of inclusion of the entry in the Workspace, 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, applying them in turn to the entries in the Workspace, in the order in which they appear in the Project Table.

Entry (PyMOL)

Colors atoms according to the entry to which they belong. The scheme cycles through the list of colors used in PyMOL, applying them in turn to the entries in the Workspace, in the order in which they appear in the Project Table.

Entry ID

Colors atoms according to the entry ID of the entry to which they belong. The scheme uses a list of 24 colors, applying them by the value of the entry ID, modulo 24: thus, each entry whose remainder when the entry ID is divided by 24 has the same color.

Hydrophobicity

Three schemes for hydrophobicity are available: Li-Tang-Wingreen (Phys. Rev. Lett. 1997, 79, 765), Kyte-Doolittle (J. Mol. Biol 1982157, 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.

Hydrophobicity - Li-Tang-Wingreen scheme.
Color ASL definition Description
all atom without PDB residue name
res.ptype leu, phe, ile, met, val q-value -0.45 to -.31 (LFIMV)
res.ptype trp, cys, tyr q-value -0.30 to -0.21 (WCY)
res.ptype ala, his q-value -0.20 to -0.11 (AH)
res.ptype thr, pro, gly, asn, arg, ser q-value -0.10 to 0.0 (TPGNRS)
res.ptype gln, asp, glu, lys q-value 0.01 to 0.07 (QDEK)

Hydrophobicity - Kyte-Doolittle scheme.
Color ASL definition Description
all atom without PDB residue name
res.ptype ile, val, leu, phe Hydropathy 4.5 to 2.8 (IVLF)
res.ptype cys, met, ala Hydropathy 2.7 to 1.0 (CMA)
res.ptype gly, thr, ser Hydropathy 0.9 to -0.8 (GTS)
res.ptype trp, tyr, pro Hydropathy -0.9 to -2.6 (WYP)
res.ptype his, asn, asp, glu, gln, arg, lys Hydropathy -2.7 to -4.5 (HNQDEKR)

Hydrophobicity - Black-Mould scheme.
Color ASL definition Description
all atom without PDB residue name
res.ptype phe, leu, ile, tyr, trp, val calc. logP 1.0 to 0.8 (FLIYWV)
res.ptype met, cys, pro, ala calc. logP 0.8 to 0.6 (MPCA)
res.ptype gly, thr, calc. logP 0.6 to 0.4 (GT)
res.ptype ser, lys, gln, asn calc. logP 0.4 to 0.2 (SKQN)
res.ptype his, glu, asp, arg calc. logP 0.2 to 0.0 (HEDR)
Molecule Number

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

Molecule Size

Colors atoms by molecule size, making it easier to locate ligands in a structure.

PDB Conversion Status

Colors residues in structures imported from the PDB by the status of their conversion, which may indicate a need for correction. The use of this scheme to color PDB structures on import is controlled by a preference.

Color Meaning
orange Nonstandard residues connected by geometry and/or CONECT records. Unless duplicate CONECT records are specified, only single order bonds are added, so multiple bonds will need to be added.
red Standard residue, but the input PDB file had missing atoms.
blue A standard residue that has some atom names unknown to the standard connection template. The unrecognized atom names were connected by geometry.
cyan An adjacent residue is listed in the SEQRES records but is entirely missing from the ATOM records, indicating a gap in the structure. A loop prediction may be necessary to fill in the missing residues.
green A residue with alternate positions for some of its atoms.
gray Standard residues connected by standard templates. Confidence in bond orders assigned to these residues is high.
Residue Charge

Colors amino acid residues according to charge. Positive charges are blue, negative charges are red.

Residue Position

Colors amino acid residues by residue number. The first 10% (including the N-terminus) of the residues in a chain are red, the last 10% (C-terminus) are purple, and there is a rainbow color ramp between those ends.

Residue Position (PyMOL)

Colors amino acid residues by residue number, using the same scheme as in PyMOL, with a rainbow color ramp from blue to red.

Residue Property

Colors amino acid residues according to hydrophobicity, charge, and polarity.

Residue Property scheme.
Color ASL definition Description
all GLY and atoms without PDB Residue names
res. ALA, CYS, ILE, LEU, MET, PHE, TRP, TYR, VAL, PRO hydrophobic ( ALA, CYS, ILE, LEU, MET, PHE, TRP, TYR, VAL, PRO )
res. SER, THR, HIS, GLN, ASN, ARN, ASH,GLH,LYN,HIE polar uncharged (SER, THR, HIS, HIE, GLN, ASN, ARN, ASH, GLH, LYN)
res. LYS, ARG,HIP Positives ( LYS, ARG, HIP )
res. ASP, GLU Negatives( ASP, GLU )
res. " G", " DG", " A", " DA", " I", " DI" Purine( G, A, I )
res. " C", " DC", " T", " DT", " U", " DU" Pyrimidine( C, T, U )
Residue Type

Colors amino acid residues by residue type.

Residue Type scheme.
Color ASL definition Description
all Unknown residues
res. ALA, PHE, ILE, LEU, MET, VAL, TYR ALA, PHE, ILE, LEU, MET, VAL, TYR
res. LYS, ARG, " T", " DT", ARN, LYN LYS, ARG, LYN, ARN, T
res. GLN, ASN GLN, ASN
res. ASP, GLU, ASH, GLH," A", " DA" ASP, GLU, A,GLH, ASH
res. CYS, " C", " DC" CYS, C
res. GLY GLY
res. HIS, HIP, HIE, " U", " DU" HIS, HIE, HIP, U
res. PRO PRO
res. SER, THR SER, THR
res. TRP, " G", " DG" TRP, G
atom.mtype ow H2O
Residue Type (spectrum)

Colors amino acid residues by residue type, with finer distinctions between conservatively mutated and conserved residues, and atoms in non-residues colored by element or periodic table block.

Residue Type (spectrum) scheme.
Color ASL definition Description
all Unknown residues
res. ALA ALA
res. PHE PHE
res. ILE or res. " A" or res. " DA" ILE, A
res. LEU LEU
res. MET MET
res. VAL VAL
res. TYR TYR
res. LYS or res. LYN or res. " C" or res. " DC" LYS, C
res. ARG or res. ARN ARG
res. GLN GLN
res. ASN ASN
res. ASP or res. ASH ASP
res. GLU or res. GLH or res. " T" or res. " DT" GLU, T
res. CYS CYS
res. GLY GLY
res. HIS or res. HIE or res. HIP or res. " U" or res. " DU" HIS, U
res. PRO PRO
res. SER or res. " G" or res. " DG" SER, G
res. THR THR
res. TRP or res. TRY TRP
atom.mtype ow H2O
atom.ele H Hydrogen (H)
atom.ele B Boron (B)
atom.ele N Nitrogen (N)
atom.ele O Oxygen (O)
atom.ele F Fluorine (F)
atom.ele Si Silicon (Si)
atom.ele P Phosphorus (P)
atom.ele S Sulfur (S)
atom.ele Cl Chlorine (Cl)
atom.ele Br Bromine (Br)
atom.ele I Iodine (I)
atom.atomic 3, 11, 19, 37, 55, 87 Alkali Metals: (Li, Na, K, Rb, Cs, Fr)
atom.atomic 4, 12, 20, 38, 56, 88 Alkali-Earth Metals: (Be, Mg, Ca, Sr, Ba, Ra)
atom.atomic 2, 10, 18, 36, 54, 86 Group Eight Elements: (He, Ne, Ar, Kr, Xe, Rn)
atom.atomic 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 First Row Transition Metals: (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn)
atom.atomic 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 Second Row Transition Metals: (Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd)
atom.atomic 72, 73, 74, 75, 76, 77, 78, 79, 80 Third Row Transition Metals: (Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg)
atom.atomic 13, 31, 32, 49, 50, 51, 81, 82, 83, 84 Post Transition Metals: (Al, Ga, Ge, In, Sn, Sb, Tl, Pb, Bi, Po)
atom.atomic 33, 34, 52, 85 Other Main Group elements: (As, Se, Te, At)
atom.atomic 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 Lanthanide Series: (La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu)
atom.atomic 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103 Actinide Series: (Ac, Th, Pa, U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr)
atom.atomic 104, 105, 106 Heavy elements: (Rf, Ha, ...)
Secondary Structure

Colors residues according to protein secondary structure (strand, loop, helix). To assign secondary structure, choose Assign Secondary Structure from the Tools menu.

Secondary Structure scheme.
Color ASL definition Description
all None assigned
res.sec helix Helix
res.sec strand Strand
res.sec loop Loop