Support for isotopes

Jmol supports isotopes; they are identified when reading files (see supported formats below) and they can be selected using atom expressions. In addition, Jmol renders the most common isotopes in different colors (lighter and heavier isotopes receive, respectively, lighter and darker shades of the standard CPK color for the element).

Atom expressions

The general syntax is to prefix the element symbol with the isotopic mass. Examples: _14C, _2H, _31P. As special cases, deuterium, tritium, _D, _T are also recognized (not valid for other elements).

Examples:

• select _H will select all hydrogen isotopes; synonym: select hydrogen
• select _1H will select only ¹H (protium)
• select _2H will select only ²H; synonyms: select deuterium, select _D
• select _3H will select only ³H; synonyms: select tritium, select _T

CML format

In the Chemical Markup Language, an isotope is specified with a string isotope= inside the <atom tag, just before the x2= or x3= parameter. Jmol supports this piece of information.

Example:

<atom id="a1" elementType="C" isotope="14" x3="0.1853" y3="0.0096" z3="0.4587"/>

MOL formats

This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like mol, sdf, etc.

There are two methods to specify an isotope in the CTfile specification. Jmol supports the first one:

1. (supported by Jmol) Including the mass difference in the atom line, columns 35-36. Mass difference is the isotope mass minus the naturally abundant mass.

Example, for ¹⁵N (15-14 = 1):

5.2002 0.7282 3.0988 N 1 0 0 0 0 0 0 0 0 0 0 0

Example, for ¹⁴C (14-12 = 2):

5.2002 0.7282 3.0988 C 2 0 0 0 0 0 0 0 0 0 0 0

Example, for ¹¹C (11-12 = -1):

5.2002 0.7282 3.0988 C -1 0 0 0 0 0 0 0 0 0 0 0

2. (not supported by Jmol) Stating the isotope mass in an "M ISO" line at the end of the file, columns 15-16.

Example, for ¹⁵N:

M ISO 1 7 15

Example, for ¹⁴C:

M ISO 1 7 14

The "1" indicates the number of entries in the line. The "7" is the affected atom's serial number in the file.

MOL V3000 formats

This includes all formats based on the V3000 chemical table files (CTfiles) specification from MDL/Symyx, like mol, sdf, etc.

Jmol supports the V3000 CTfile specification which sets an isotope mass in the atom line.

Example, for ¹⁵N :

M V30 3 N -0.7207 2.0817 0 0 MASS=15

PDB format

D and T are recognized as element identifiers, both in the atom name field (column 14) and in the element field (column 78). There is no way in pdb format to specify isotopes for other elements.

CIF format

D and T are recognized as element identifiers, in the _atom_site_type_symbol field. There is no support for other isotopes.

XYZ format

Although not a standard feature of xyz, Jmol will accept a special extension of the format¹ where the isotope mass prefixes the element symbol.

Example:

13C 3.4 5.6 7.8

C 2.3 4.4 4.4

12C 3.2 3.3 3.3

¹ Bob Hanson, 25 Sep 2006, jmol-users list. A new file format: "isotope-xyz" or XYZI.

HIN format

Similarly to xyz format, if the isotope mass prefixes the element symbol, Jmol will read that isotope.

Example:

atom 4 - C CA - -1 0.8030124 0.6530771 0 3 3 a 5 a 10 s

atom 5 - 14C CA - 0 0.8030125 -0.7433776 0 3 4 a 6 a 11 s

atom 6 - D H - 0 -0.4063521 2.45442 0 1 3 s

Contributors

AngelHerraez