VDW Radii

Atomic VDW (van der Waals) radii are used in sphere and ball display. They are also used to identify clashes and contacts and to calculate molecular surfaces and surface areas. VDW radii are assigned automatically based on atom types (or read directly from the input file, if PQR) and can be changed with the size command. The VDW radius of an atom may also change as a side effect of changing its atom type or number of attached hydrogens. The values are stored as the atom attribute named radius. See also: surface, measure, interfaces, setattr, attribute assignment examples

Default Assignments

For C, N, O, and S, the default VDW radii depend on whether explicit hydrogen atoms are present:

When a molecule model has no explicit hydrogens, “united-atom” radii based on the ProtOr set are used:
The packing density in proteins: standard radii and volumes. Tsai J, Taylor R, Chothia C, Gerstein M. J Mol Biol. 1999 Jul 2;290(1):253-66.
When there are explicit hydrogens, “all-atom” radii derived from the Amber parm99 parameters are used for the filled-valence atoms. United-atom radii are used for any atoms with unfilled valence (those apparently missing hydrogens).

Due to differences in how the sets were derived, united-atom radii are not always larger than the corresponding all-atom radii.

For metal and halide ions, ionic radii from The CRC Handbook of Chemistry and Physics, 82nd Edition (2001-2002) are used. If the charge state differs from that listed below, a different radius may be more appropriate.

For P, and for F, Cl, Br, and I in the context of molecules (as opposed to singleton ions), the all-atom radii are used.

The default VDW radii of any remaining atoms are twice their covalent bond radii.

Default VDW Radii

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United-Atom Radii
atom description (see also atom type)	# hydrogens attached	radius (Å)
sp² C	0	1.61^a
sp² C	1	1.76^a
sp³ C	1-3	1.88^a
any other C		1.88
sp² N	0-2	1.64^a
sp³ N	3	1.64^a
any other N		1.64
sp² O	0	1.42^a
sp³ O	1	1.46^a
sp³ O	0	1.46
any other O		1.42
sp³ S	0-1	1.77^a
any other S		1.77

^a Tsai et al., J Mol Biol 290:253 (1999)

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All-Atom Radii
atom description (see also atom type)	Amber atom type	radius (Å)^b
C	all C types	1.700
N	all N types	1.625
sp² O	O, O2	1.480
sp³ O	OS	1.500
S	S, SH	1.782
H	(see note^c)	1.000
P	P	1.871
F	F	1.560
Cl	Cl	1.735
Br	Br	1.978
I	I	2.094

^b Derived from the Amber parm99 parameters: R_VDW = (R*)/(2^1/6)
^c Amber parm99 includes many H types with VDW radii ranging from 0.0 to 1.325 Å; smaller radii are assigned to hydrogens bonded to more electron-withdrawing moieties. The atom types only distinguish between hydrogen bonded to carbon and hydrogen bonded to “other,” so a compromise value of 1.0 has been used for all hydrogens.

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Selected Ionic Radii
ion	coordination number (default in bold)	radius (Å)^d
Al⁺³	4 5 6	0.39 0.48 0.54
As⁺³	6	0.58
Au⁺¹	6	1.37
Ba⁺²	6 8 12	1.35 1.42 1.61
Be⁺²	4 6	0.27 0.45
Bi⁺³	5 6 8	0.96 1.03 1.17
Ca⁺²	6 8 10 12	1.00 1.12 1.23 1.34
Cd⁺²	4 6 8 12	0.78 0.95 1.10 1.31
Co⁺²	4 6 8	0.56 0.65 0.90
Cr⁺²	6	0.73
Cs⁺	6 8 10 12	1.67 1.74 1.81 1.88
Cu⁺²	4 6	0.57 0.73
Fe⁺²	4 6 8	0.63 0.61 0.92
Ga⁺³	4 6	0.47 0.62
Ge⁺²	6	0.73
Hg⁺²	2 4 6 8	0.69 0.96 1.02 1.14
K⁺	4 6 8 12	1.37 1.38 1.51 1.64
Li⁺	4 6 8	0.59 0.76 0.92
Mg⁺²	4 6 8	0.57 0.72 0.89
Mn⁺²	4 6 8	0.66 0.83 0.96
Mo⁺³	6	0.69
Na⁺	4 6 8 9 12	0.99 1.02 1.18 1.24 1.39
Ni⁺²	4 6	0.49 0.69
Pb⁺²	6 8 10 12	1.19 1.29 1.40 1.49
Pd⁺²	4 6	0.64 0.86
Pt⁺²	4 6	0.60 0.80
Rb⁺	6 8 10 12	1.52 1.61 1.66 1.72
Sb⁺³	4 6	0.76 0.76
Sc⁺³	6 8	0.75 0.87
Sn⁺⁴	4 6 8	0.55 0.69 0.81
Sr⁺²	6 8 10 12	1.18 1.26 1.36 1.44
Tc⁺⁴	6	0.65
Ti⁺²	6	0.86
V⁺²	6	0.79
Zn⁺²	4 6 8	0.60 0.74 0.90
Zr⁺⁴	4 6 8 9	0.59 0.72 0.84 0.89
F^–	6	1.33
Cl^–	6	1.81
Br^–	6	1.96
I^–	6	2.20

^d CRC Handbook of Chemistry and Physics, 82nd Edition (2001-2002). Additional ionic radii from the same reference (for more rarely encountered ions) are also used as defaults in ChimeraX, but not listed above.

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2020