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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


next up gif contents index
Next: Font mapping for Raster3D Up: SPOCK: The Structural Properties Previous: Pre-defined Sets

Jon Christopher
Tue Sep 14 16:44:48 CDT 1999