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>. As | + | 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> | + | * <code>select _H</code> will select all hydrogen isotopes; synonym: <code>select hydrogen</code> |
| − | * <code>select _2H</code> | + | * <code>select _1H</code> will select only <sup>1</sup>H (protium) |
| − | * <code>select | + | * <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 == | ||
| + | In the Chemical Markup Language, an isotope is specified with a string <tt>isotope=</tt> inside the <tt><atom</tt> tag, just before the <tt>x2=</tt> or <tt>x3=</tt> parameter. Jmol supports this piece of information. | ||
| + | :Example: | ||
| + | :<tt><atom id="a1" elementType="C" isotope="14" x3="0.1853" y3="0.0096" z3="0.4587"/></tt> | ||
== MOL formats == | == MOL formats == | ||
| Line 21: | Line 27: | ||
:<tt> 5.2002 0.7282 3.0988 C '''-1''' 0 0 0 0 0 0 0 0 0 0 0</tt> | :<tt> 5.2002 0.7282 3.0988 C '''-1''' 0 0 0 0 0 0 0 0 0 0 0</tt> | ||
| − | 2. ''( | + | 2. ''(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: | :Example, for <sup>15</sup>N: | ||
:<tt>M ISO 1 7 '''15''' </tt> | :<tt>M ISO 1 7 '''15''' </tt> | ||
| Line 27: | Line 33: | ||
:<tt>M ISO 1 7 '''14''' </tt> | :<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. | :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 <code>mol</code>, <code>sdf</code>, etc.'' | ||
| + | |||
| + | Jmol supports the V3000 CTfile specification which sets an isotope mass in the atom line. | ||
| + | :Example, for <sup>15</sup>N : | ||
| + | :<tt>M V30 3 N -0.7207 2.0817 0 0 MASS=15</tt> | ||
== PDB format == | == 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). | 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. | There is no way in <code>pdb</code> format to specify isotopes for other elements. | ||
| + | |||
| + | == CIF format == | ||
| + | D and T are recognized as element identifiers, in the <code>_atom_site_type_symbol</code> field. There is no support for other isotopes. | ||
== XYZ format == | == XYZ format == | ||
| − | Although not a standard feature of <code>xyz</code>, Jmol will accept a special extension of the format< | + | 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: | :Example: | ||
:<tt>13C 3.4 5.6 7.8</tt> | :<tt>13C 3.4 5.6 7.8</tt> | ||
| Line 39: | Line 55: | ||
:<tt>12C 3.2 3.3 3.3</tt> | :<tt>12C 3.2 3.3 3.3</tt> | ||
| + | <sup>1</sup> Bob Hanson, 25 Sep 2006, jmol-users list. A new file format: "isotope-xyz" or XYZI. | ||
| − | + | == HIN format == | |
| − | + | Similarly to <code>xyz</code> format, if the isotope mass prefixes the element symbol, Jmol will read that isotope. | |
| − | < | + | :Example: |
| + | :<tt>atom 4 - C CA - -1 0.8030124 0.6530771 0 3 3 a 5 a 10 s </tt> | ||
| + | :<tt>atom 5 - 14C CA - 0 0.8030125 -0.7433776 0 3 4 a 6 a 11 s </tt> | ||
| + | :<tt>atom 6 - D H - 0 -0.4063521 2.45442 0 1 3 s </tt> | ||
Latest revision as of 17:39, 28 April 2017
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).
Contents
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 _Hwill select all hydrogen isotopes; synonym:select hydrogenselect _1Hwill select only 1H (protium)select _2Hwill select only 2H; synonyms:select deuterium,select _Dselect _3Hwill 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. (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 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
