Difference between revisions of "Support for isotopes"
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== Atom expressions == | == Atom expressions == | ||
| − | The general syntax is to prefix the element symbol with the isotopic mass. Examples: <code>_14C</code>, <code>_2H</code>, <code>_31P</code>. | + | The general syntax is to prefix the element symbol with the isotopic mass. Examples: <code>_14C</code>, <code>_2H</code>, <code>_31P</code>. As a special case, <code>deuterium</code>, <code>tritium</code>, <code>_D</code>, <code>_T</code> are also recognized (not for other elements). |
:Examples: | :Examples: | ||
* <code>select _H</code> will select all hydrogen isotopes | * <code>select _H</code> will select all hydrogen isotopes | ||
| − | * <code>select _2H</code> will select only <sup>2</sup>H (deuterium) | + | * <code>select _2H</code> will select only <sup>2</sup>H (deuterium); synonyms: <code>select deuterium</code>, <code>select _D</code> |
| − | * <code>select _H and not (_2H,_3H)</code> will select only protium (<sup>1</sup>H) | + | * <code>select _H and not (_2H,_3H)</code> will select only protium (<sup>1</sup>H); for that, you can also do <code>select _1H</code> |
== MOL formats == | == MOL formats == | ||
Revision as of 16:01, 6 April 2009
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. As a special case, deuterium, tritium, _D, _T are also recognized (not for other elements).
- Examples:
select _Hwill select all hydrogen isotopesselect _2Hwill select only 2H (deuterium); synonyms:select deuterium,select _Dselect _H and not (_2H,_3H)will select only protium (1H); for that, you can also doselect _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.
