Difference between revisions of "Support for isotopes"

From Jmol
Jump to navigation Jump to search
(MOLv3000 and CML)
(→‎Atom expressions)
Line 2: Line 2:
  
 
== 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>. As a special case, <code>deuterium</code>, <code>tritium</code>, <code>_D</code>,  <code>_T</code> are also recognized (not for other elements).
+
The general syntax is to prefix the element symbol with the isotopic mass. Examples: <code>_14C</code>, <code>_2H</code>, <code>_31P</code>. As special cases, <code>deuterium</code>, <code>tritium</code>, <code>_D</code>,  <code>_T</code> are also recognized (not valid for other elements).
 
:Examples:
 
:Examples:
−
* <code>select _H</code> will select all hydrogen isotopes
+
* <code>select _H</code> will select all hydrogen isotopes; synonym: <code>select hydrogen</code>
−
* <code>select _2H</code> will select only <sup>2</sup>H (deuterium); synonyms: <code>select deuterium</code>, <code>select _D</code>
+
* <code>select _1H</code> will select only <sup>1</sup>H (protium)
−
* <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>
+
* <code>select _2H</code> will select only <sup>2</sup>H; synonyms: <code>select deuterium</code>, <code>select _D</code>
 +
* <code>select _3H</code> will select only <sup>3</sup>H; synonyms: <code>select tritium</code>, <code>select _T</code>
  
 
== CML format ==
 
== CML format ==

Revision as of 20:00, 18 April 2009

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.

XYZ format

Although not a standard feature of xyz, Jmol will accept a special extension of the format[1] 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.

Contributors

AngelHerraez

Retrieved from "https://wiki.jmol.org/index.php?title=Support_for_isotopes&oldid=5660"