Support for isotopes

Jmol supports isotopes; isotopes 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 (heavier isotopes receive 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. The names deuterium and tritium are also recognized.

Examples:

• select _H will select all hydrogen isotopes
• select _2H will select only ²H (deuterium)
• select _H and not (_2H,_3H) will select only protium (¹H)

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:

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

Example, for ¹⁴C:

5.2002 0.7282 3.0988 C 2 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.

Contributors

AngelHerraez