Internal Periodic Table/Default Radii and Default Colors

This information is mostly for internal use, although the atom type can be used as a selection parameter via the element= query string. Atom types are generally taken from the first two letters of the PDB atom name, however if an atom is not from a HETERO record only CA,H,C,N,O,P and S are allowed. Although the PDB specification states that the first two columns are reserved for the atomic symbol, that is not always followed, so some structures may have mis-identified atoms.

Below are the atom types, the default radii, and colors. These values can be changed via the define element command, §5.2.6. 1cm

Atom Covalent VdW Color Name Mass

C 0.68 1.55 1 Alpha-CARBON 12.011

H 0.32 1.10 06 HYDROGEN 1.007

HE 1.60 2.20 10 HELIUM 4.002

LI 0.68 1.22 10 LITHIUM 6.941

BE 0.35 0.63 10 BERYLLIUM 9.012

B 0.82 1.55 10 BORON 10.811

C 0.68 1.55 01 CARBON 12.011

N 0.75 1.40 04 NITROGEN 14.006

O 0.73 1.35 02 OXYGEN 15.999

F 0.72 1.30 10 FLUORINE 18.998

NE 1.12 2.02 10 NEON 20.179

NA 0.97 2.20 10 SODIUM 22.989

MG 1.10 1.50 10 MAGNESIUM 24.305

AL 1.35 1.50 10 ALUMINUM 26.981

SI 1.20 2.20 10 SILICON 28.085

P 1.05 1.88 07 PHOSPHORUS 30.973

S 1.02 1.81 05 SULPHUR 32.066

CL 0.99 1.75 10 CHLORINE 35.452

AR 1.57 2.77 10 ARGON 39.948

K 1.33 2.39 10 POTASSIUM 39.098

CA 0.99 1.95 10 CALCIUM 40.078

SC 1.44 1.32 10 SCANDIUM 44.955

TI 1.47 1.95 10 TITANIUM 47.867

V 1.33 1.06 10 VANADIUM 50.941

CR 1.35 1.13 10 CHROMIUM 51.996

MN 1.35 1.19 10 MANGANESE 54.938

FE 1.34 1.95 10 IRON 55.845

CO 1.33 1.13 10 COBALT 58.933

NI 1.50 1.24 10 NICKEL 58.693

CU 1.52 1.15 10 COPPER 63.546

ZN 1.45 1.15 10 ZINC 65.39

GA 1.22 1.55 10 GALLIUM 69.723

GE 1.17 4.00 10 GERMANIUM 72.61

AS 1.21 0.83 10 ARSENIC 74.921

SE 1.22 0.90 10 SELENIUM 78.96

BR 1.21 1.75 10 BROMINE 79.904

KR 1.60 1.90 10 KRYPTON 83.80

RB 1.47 2.65 10 RUBIDIUM 85.467

SR 1.12 2.02 10 STRONTIUM 87.62

Y 1.78 1.61 10 YTTRIUM 88.905

ZR 1.56 1.42 10 ZIRCONIUM 91.224

NB 1.48 1.33 10 NIOBIUM 92.906

MO 1.47 1.75 10 MOLYBDENUM 95.94

TC 1.35 1.80 10 TECHNETIUM 98.0

RU 1.40 1.20 10 RUTHENIUM 101.07

RH 1.45 1.22 10 RHODIUM 102.905

PD 1.50 1.44 10 PALLADIUM 106.42

AG 1.59 1.55 10 SILVER 107.868

CD 1.69 1.75 10 CADMIUM 112.411

IN 1.63 1.45 10 INDIUM 114.818

SN 1.46 1.67 10 TIN 118.710

SB 0.62 1.12 10 ANTIMONY 121.760

Atom Covalent VdW Color Name Mass

TE 0.70 1.26 10 TELLURIUM 127.60

I 1.40 1.75 10 IODINE 126.904

XE 1.70 2.10 10 XENON 131.29

CS 1.67 3.01 10 CESIUM 132.905

BA 1.34 2.41 10 BARIUM 137.327

LA 1.02 1.83 10 LANTHANUM 138.905

CE 1.03 1.86 10 CERIUM 140.115

PR 0.90 1.62 10 PRASEODYMIUM 140.907

ND 0.99 1.79 10 NEODYMIUM 144.24

PM 0.98 1.76 10 PROMETHIUM 145.0

SM 0.96 1.74 10 SAMARIUM 150.36

EU 1.09 1.96 10 EUROPIUM 151.965

GD 0.94 1.69 10 GADOLINIUM 157.25

TB 0.92 1.66 10 TERBIUM 158.925

DY 0.91 1.63 10 DYSPROSIUM 162.50

HO 0.89 1.61 10 HOLMIUM 164.930

ER 0.88 1.59 10 ERBIUM 167.26

TM 0.87 1.57 10 THULIUM 168.934

YB 0.86 1.54 10 YTTERBIUM 173.04

LU 0.85 1.53 10 LUTETIUM 174.967

HF 0.78 1.40 10 HAFNIUM 178.49

TA 0.68 1.22 10 TANTALUM 180.947

W 0.70 1.26 10 TUNGSTEN 183.84

RE 0.72 1.30 10 RHENIUM 186.207

OS 0.88 1.58 10 OSMIUM 190.23

IR 0.68 1.22 10 IRIDIUM 192.217

PT 1.30 1.55 10 PLATINUM 195.08

AU 1.34 1.45 10 GOLD 196.966

HG 1.10 1.98 10 MERCURY 200.59

TL 0.95 1.71 10 THALLIUM 204.383

PB 1.20 2.16 10 LEAD 207.2

BI 0.96 1.73 10 BISMUTH 208.980

PO 0.67 1.21 10 POLONIUM 209.0

AT 0.62 1.12 10 ASTATINE 210.0

RN 1.90 2.30 10 RADON 222.0

FR 1.80 3.24 10 FRANCIUM 223.0

RA 1.43 2.57 10 RADIUM 226.0

AC 1.18 2.12 10 ACTINIUM 227.0

TH 1.02 1.84 10 THORIUM 232.038

PA 0.89 1.60 10 PROTACTINIUM 231.035

U 0.97 1.75 10 URANIUM 238.028

NP 0.95 1.71 10 NEPTUNIUM 237.0

PU 0.93 1.67 10 PLUTONIUM 244.0

AM 0.92 1.66 10 AMERICIUM 243.0

CM 0.91 1.65 10 CURIUM 247.0

BK 0.90 1.64 10 BERKELIUM 247.0

CF 0.89 1.63 10 CALIFORNIUM 251.0

ES 0.88 1.62 10 EINSTEINIUM 252.0

FM 0.87 1.61 10 FERMIUM 257.0

MD 0.86 1.60 10 MENDELEVIUM 258.0

NO 0.85 1.59 10 NOBELIUM 259.0

LR 0.84 1.58 10 LAWRENCIUM 262.0