Support for isotopes - Revision history

AngelHerraez: MOL/SDF reader reads M ISO lines for isotopes (Jmol 14.15.1)

2017-04-28T17:39:44Z

MOL/SDF reader reads M ISO lines for isotopes (Jmol 14.15.1)

AngelHerraez: isotopes in CIF files

2011-09-03T15:58:05Z

isotopes in CIF files

AngelHerraez: Fix reference tag in XYZ. Add HIN section.

2010-06-03T16:40:03Z

Fix reference tag in XYZ. Add HIN section.

AngelHerraez: /* Atom expressions */

2009-04-18T20:00:21Z

‎Atom expressions

AngelHerraez: MOLv3000 and CML

2009-04-09T19:19:59Z

MOLv3000 and CML

AngelHerraez at 16:33, 6 April 2009

2009-04-06T16:33:55Z

AngelHerraez: isotopes in XYZ format

2009-04-06T16:23:50Z

isotopes in XYZ format

AngelHerraez: /* Atom expressions */

2009-04-06T16:01:06Z

‎Atom expressions

AngelHerraez: new page for isotopes

2009-04-06T15:42:20Z

new page for isotopes

New page

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 [[Colors#Support_for_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: <code>_14C</code>, <code>_2H</code>, <code>_31P</code>. The names <code>deuterium</code> and <code>tritium</code> are also recognized.
:Examples:
* <code>select _H</code> will select all hydrogen isotopes
* <code>select _2H</code> will select only 2H (deuterium)
* <code>select _H and not (_2H,_3H)</code> will select only protium (1H)

== MOL formats ==
''This includes all formats based on the chemical table files (CTfiles) specification from MDL/Symyx, like <code>mol</code>, <code>sdf</code>, 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:
:<tt> 5.2002 0.7282 3.0988 N '''1''' 0 0 0 0 0 0 0 0 0 0 0</tt>
:Example, for 14C:
:<tt> 5.2002 0.7282 3.0988 C '''2''' 0 0 0 0 0 0 0 0 0 0 0</tt>

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:
:<tt>M ISO 1 7 '''15''' </tt>
:Example, for 14C:
:<tt>M ISO 1 7 '''14''' </tt>
:The "1" indicates the number of entries in the line. The "7" is the affected atom's serial number in the file.

@@ Line 27: / Line 27: @@
 :<tt>    5.2002    0.7282    3.0988 C  '''-1'''  0  0  0  0  0  0  0  0  0  0  0</tt>
-. ''(not supported by Jmol)'' Stating the isotope mass in an "M ISO" line at the end of the file, columns 15-16.
+. ''(supported by Jmol since v. 14.15.1)'' Stating the isotope mass in an "M ISO" line at the end of the file, columns 15-16.
 :Example, for <sup>15</sup>N:
 :<tt>M ISO  1   7  '''15''' </tt>

@@ Line 44: / Line 44: @@
 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 <code>pdb</code> format to specify isotopes for other elements.
 == XYZ format ==

@@ Line 46: / Line 46: @@
 == XYZ format ==
-Although not a standard feature of <code>xyz</code>, Jmol will accept a special extension of the format<ref>Bob Hanson, 25 Sep 2006, jmol-users list. A new file format: "isotope-xyz" or XYZI.</ref> where the isotope mass prefixes the element symbol.
+Although not a standard feature of <code>xyz</code>, Jmol will accept a special extension of the format<sup>1</sup> where the isotope mass prefixes the element symbol.
 :Example:
 :<tt>13C    3.4   5.6   7.8</tt>
@@ Line 52: / Line 52: @@
 :<tt>12C    3.2   3.3   3.3</tt>
+== HIN format ==
+Similarly to <code>xyz</code> format, if the isotope mass prefixes the element symbol, Jmol will read that isotope.
-<references/>
+:Example:

@@ Line 2: / Line 2: @@
 == 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:
-* <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>
 == CML format ==

@@ Line 7: / Line 7: @@
 * <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); for that, you can also do <code>select _1H</code>
 == MOL formats ==
@@ Line 27: / Line 32: @@
 :<tt>M ISO  1   7  '''14''' </tt>
 :The "1" indicates the number of entries in the line. The "7" is the affected atom's serial number in the file.
 == PDB format ==

@@ Line 1: / Line 1: @@
-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 [[Colors#Support_for_isotopes |in different colors]] (heavier isotopes receive darker shades of the standard CPK color for the element).
+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 [[Colors#Support_for_isotopes |in different colors]] (lighter and heavier isotopes receive, respectively, lighter and darker shades of the standard CPK color for the element).
 == Atom expressions ==
@@ Line 14: / Line 14: @@
 . ''(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 <sup>15</sup>N:
+:Example, for <sup>15</sup>N  (15-14 = 1):
 :<tt>    5.2002    0.7282    3.0988 N   '''1'''  0  0  0  0  0  0  0  0  0  0  0</tt>
-:Example, for <sup>14</sup>C:
+:Example, for <sup>14</sup>C  (14-12 = 2):
 :<tt>    5.2002    0.7282    3.0988 C   '''2'''  0  0  0  0  0  0  0  0  0  0  0</tt>
 . ''(not supported by Jmol)'' Stating the isotope mass in an "M ISO" line at the end of the file, columns 15-16.