File formats/Formats/XYZ - Revision history

AngelHerraez at 15:48, 28 November 2021

2021-11-28T15:48:51Z

AngelHerraez: xyz format with text in the 2nd line

2016-09-26T15:02:54Z

xyz format with text in the 2nd line

AngelHerraez: xyz format with text in the 2nd line

2016-09-26T14:38:18Z

xyz format with text in the 2nd line

AngelHerraez: XYZ: moving detailed info to new subpage

2010-06-02T23:34:30Z

XYZ: moving detailed info to new subpage

AngelHerraez: XYZ: moving detailed info to new subpage

2010-06-02T23:33:29Z

XYZ: moving detailed info to new subpage

New page

= The XYZ file format =

==Description==
XYZ datafiles specify molecular geometries using a Cartesian coordinate system. This simple, stripped-down, ASCII-readable format is intended to serve as a "transition" format for the XMol series of applications. For example, suppose a molecular datafile was in a format not supported by XMol. In order to read the data into XMol, it would be possible to modify the datafile, perhaps by creating a shell script, so that it fit the relatively lenient requirements of the XYZ format specification. Once data is in XYZ format, it may be examined by XMol, or converted to yet another format.

The XYZ format supports '''multi-step datasets'''. '''Each step''' is represented by a two-line "header," followed by one line for each atom.

The '''first line''' of a step's header is the number of atoms in that step. This integer may be preceded by whitespace; anything on the line after the integer is ignored.

The '''second line''' of the header leaves room for a descriptive string. This line may be blank, or it may contain some information pertinent to that particular step, but it must exist, and it must be just one line long.

'''Each line of text describing a single atom''' must contain at least four fields of information, separated by whitespace: the atom's type (a short string of alphanumeric characters), and its x-, y-, and z-positions. Optionally, extra fields may be used to specify a charge for the atom, and/or a vector associated with the atom. If an input line contains five or eight fields, the fifth field is interpreted as the atom's charge; otherwise, a charge of zero is assumed. If an input line contains seven or eight fields, the last three fields are interpreted as the components of a vector. These components should be specified in angstroms.

Note that the XYZ format doesn't contain '''connectivity''' information. This intentional omission allows for greater flexibility: to create an XYZ file, you don't need to know where a molecule's bonds are; you just need to know where its atoms are. Connectivity information is generated automatically for XYZ files as they are read into XMol-related applications. Briefly, if the distance between two atoms is less than the sum of their covalent radii, they are considered bonded.

The XYZ reader in Jmol reads any of the following (updated for Jmol v. 11.4.5 and 11.5.41):
<pre>
Sym x y z
Sym x y z vibX vibY vibZ
Sym x y z FormalCharge(integer)
Sym x y z FormalCharge(integer) vibX vibY vibZ
Sym x y z PartialCharge(decimal)
Sym x y z PartialCharge(decimal) vibX vibY vibZ
</pre>
:where <code>Sym</code> is either an element symbol (C, Fe, Si) or an element symbol preceded by a supported isotope number (2H, 13C, etc.)

= Sources =
* Man page for XYZ (part of XMol), quoted at http://www.ccl.net/chemistry/resources/messages/1996/10/21.005-dir/index.html

@@ Line 9: / Line 9: @@
 : Note, however, that if there is any text after the number Jmol will '''''not''''' automatically recognize it as an <code>xyz</code>-formatted file; in that case, you need to explicitly indicate the format in the <code>load</code> command, like this:
 :<code>load xyz::myFile.xyz</code>
-: That given, the presence of any text after the number in the 2nd line will not affect proper file reading.
+: That given, the presence of any text after the number in the 1st line will not affect proper file reading.
 The '''second line''' of the header leaves room for a descriptive string. This line may be blank, or it may contain some information pertinent to that particular step, but it must exist, and  it must be just one line long.

@@ Line 7: / Line 7: @@
 The '''first line''' of a step's header is the number of atoms in that step. This  integer  may be preceded by whitespace; anything on the line after the integer is ignored.
-: Note, however, that if there is any text after the number Jmol will not automatically recognize it as an <code>xyz</code>-formatted file; in that case, you need to explicitly indicate the format in the <code>load</code> command, like this:
+: Note, however, that if there is any text after the number Jmol will '''''not''''' automatically recognize it as an <code>xyz</code>-formatted file; in that case, you need to explicitly indicate the format in the <code>load</code> command, like this:
 :<code>load xyz::myFile.xyz</code>
 : That given, the presence of any text after the number in the 2nd line will not affect proper file reading.
@@ Line 18: / Line 18: @@
 == Jmol support ==
-The XYZ reader in Jmol reads any of the following (updated for Jmol v. 11.4.5 and 11.5.41):
+The XYZ reader in Jmol reads any of the following, alternative, formats in each atom's line (updated for Jmol v. 11.4.5 and 11.5.41):
 <pre>
 Sym   x   y   z

@@ Line 1: / Line 1: @@
 = The XYZ file format =
-==Description==
+== Description ==
 XYZ datafiles specify molecular geometries using a Cartesian coordinate system. This simple, stripped-down, ASCII-readable format is intended to serve as a "transition" format for the XMol series of applications. For example, suppose a molecular datafile was in a format not supported by XMol. In order to read the data into XMol, it would be possible to modify the datafile, perhaps by creating a shell script, so that it fit the relatively lenient requirements of the XYZ format specification. Once data is in XYZ format, it may be examined by XMol, or converted to yet another format.
@@ Line 14: / Line 14: @@
 Note that the XYZ format doesn't contain '''connectivity''' information. This intentional omission allows for greater flexibility: to create an XYZ file, you don't need to know where a molecule's bonds are; you just need to know where its atoms are. Connectivity information is generated automatically for XYZ files as they are read into XMol-related applications. Briefly, if the distance between two atoms is less than the sum of their covalent radii, they are considered bonded.
 The XYZ reader in Jmol reads any of the following (updated for Jmol v. 11.4.5 and 11.5.41):
 <pre>