File formats/Coordinates - Revision history

AngelHerraez: /* SPARTAN, SMOL, SPARCHIVE */

2023-02-17T16:52:39Z

‎SPARTAN, SMOL, SPARCHIVE

AngelHerraez: /* SPARTAN, SMOL, SPARCHIVE */

2023-02-17T16:48:58Z

‎SPARTAN, SMOL, SPARCHIVE

AngelHerraez: Spartan file formats

2023-02-17T13:45:22Z

Spartan file formats

AngelHerraez: link to updated MOLfile doc

2022-09-29T15:44:33Z

link to updated MOLfile doc

AngelHerraez: /* XYZ */

2021-11-28T15:51:25Z

‎XYZ

AngelHerraez: Forcing Jmol to read a file assuming a certain molecular file format

2017-08-19T09:04:59Z

Forcing Jmol to read a file assuming a certain molecular file format

AngelHerraez: better intro

2017-08-18T18:52:44Z

better intro

AngelHerraez: file open from databases

2016-07-11T16:33:32Z

file open from databases

Pbourke: /* HIV / HIN (Hyperchem) */

2013-09-23T12:53:00Z

‎HIV / HIN (Hyperchem)

Pbourke: /* Cube (Gaussian) */

2013-09-23T12:51:53Z

‎Cube (Gaussian)

@@ Line 369: / Line 369: @@
 == SPARTAN, SMOL, SPARCHIVE ==
-These are proprietary formats of the Spartan software by [https://www.wavefun.com/support WaveFunction]
+Jmol can read these, which are proprietary formats of the Spartan software by [https://www.wavefun.com/support WaveFunction]
-They are binary files which Jmol is able to open. See [https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/spartan/ some examples].
+See [https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/spartan/ some examples] of these files.
 <br />

@@ Line 369: / Line 369: @@
 == SPARTAN, SMOL, SPARCHIVE ==
-These are propietary formats of the Spartan software by [https://www.wavefun.com/support WaveFunction]
+These are proprietary formats of the Spartan software by [https://www.wavefun.com/support WaveFunction]
 <br />

@@ Line 365: / Line 365: @@
 Kyoto Encyclopedia of Genes and Genomes ([http://www.genome.jp/kegg/ KEGG]) and the Resource for Informatics of Glycomes at Soka ([http://rings.t.soka.ac.jp/ RINGS]). It is somewhat similar to the {{file|mol}} format.
 * Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. M. Hattori, Y. Okuno, S. Goto, M. Kanehisa (2003) ''Journal of the American Chemical Society'' '''125''':11853-11865 PMID:14505407 doi:10.1021/ja036030u
-−
 = Exporting Coordinates =

@@ Line 32: / Line 32: @@
-== MOL and SD (Symyx MDL) ==
+== MOL and SD ==
 MOL = MDL molfile = MOL v2000
@@ Line 42: / Line 42: @@
 Jmol reads MOL v2000 and v3000, and SD files (and can [[File_formats/Export|write]] them too).
-Original from Molecular Design Limited, then Elsevier MDL, now Symyx Technologies, widely adopted by many other programs.
+Original from Molecular Design Limited, then Elsevier MDL, then Symyx Technologies, then BIOVIA Dassault Systèmes, widely adopted by many other programs.
 Contains atom coordinates and bonds. V2000 (the most common) is limited to 1000 atoms.
-These formats support formal charges and [[Support_for_isotopes | isotopes]]; both are read by Jmol. A variant used in PubChem adds partial charges using a custom field <code><PUBCHEM_MMFF94_PARTIAL_CHARGES></code>, and this is now also read by Jmol.
+These formats support formal charges and [[Support_for_isotopes | isotopes]]; both are read by Jmol. A variant used in PubChem adds partial charges using a custom field <code><PUBCHEM_MMFF94_PARTIAL_CHARGES></code>, and this is also read by Jmol.
 There are often MOL and SD files with two-dimensional data (i.e, all atoms have Z=0); Jmol will read them too, but the resulting flat model will not be realistic.
 The defining tag (2D or 3D) must be located in line 2, columns 21-22, but is ignored by Jmol, which just uses the Z coordinates provided, be they zero or not.
-: Jmol v.12 has two ways to deal with such flat models:
+: Jmol has two ways to deal with such flat models:
 :* you can run the [{{ScriptingDoc}}#minimize<code>minimize</code> command] after loading; this will apply a simple UFF force field to reach a reasonable 3D structure;
 :* or you can load the file using the [{{ScriptingDoc}}#loadgeneraloptions<code>filter "2D"</code> switch] of the load command, in this way:
@@ Line 61: / Line 61: @@
 * The third line is for comments, and may contain an [[#Script_inline_within_a_molecular_coordinates_file | inline script]] starting with <code>jmolscript:</code>.
-Official document (PDF): http://accelrys.com/products/informatics/cheminformatics/ctfile-formats/no-fee.php, copied [{{SVN Trunk}}Jmol-datafiles/mol/ctfile.pdf here].
+Official document (PDF):
 Some extra information on SD files at [http://www.epa.gov/ncct/dsstox/MoreonSDF.html US EPA DSSTox].

@@ Line 112: / Line 112: @@
 XYZ header lines:
 * The first line is reserved for the number of atoms.
-* The second line is for comments, and may contain an [[#Script_inline_within_a_molecular_coordinates_file | inline script]]  starting with <code>jmolscript:</code>.
+* The second line is for comments, and may contain an [[File_formats/Scripting#Script_inline_within_a_molecular_coordinates_file | inline script]]  starting with <code>jmolscript:</code>.
 [http://paulbourke.net/dataformats/xyz/ Example] by Paul Bourke.

@@ Line 17: / Line 17: @@
 where ''fileName'' includes the path, the file name itself and the file extension; paths may be absolute or relative; a full URL may also be used.
-''fileFormat'' will be a keyword recognized by Jmol that designates that format.
+''fileFormat'' will be a keyword recognized by Jmol that designates that format. (Here is a [[File_formats/LoadFormatPrefixes|list of format values]])
 Examples:

@@ Line 10: / Line 10: @@
 * using the <code>load</code> command in the command line, in the Jmol scripting console, or in a script,
 * dragging and dropping the file onto the Jmol application window
 What follows is a collection of specifications and comments on several formats, but is not a complete listing of all formats supported.
 ''Feel free to add a subsection with a description of a format you know well.''
-<br />
 == MOL and SD (Symyx MDL) ==

@@ Line 3: / Line 3: @@
 These files are loaded into Jmol by either of the following methods:
-* using the application's topbar menu, <code>File > Open</code>,
+* using the application's topbar menu,
 * using the <code>load</code> command in the command line, in the Jmol scripting console, or in a script,
 * dragging and dropping the file onto the Jmol application window

@@ Line 190: / Line 190: @@
 Jmol reads HIV (or HIN) files, the native format of Hyperchem, a software sold by [http://www.hyper.com/ Hypercube Inc.].
-[http://local.wasp.uwa.edu.au/~pbourke/dataformats/hyperchem/ Example] by Paul Bourke, and other [{{SVN Trunk}}Jmol-datafiles/hin/ example files].
+[http://paulbourke.net/dataformats/hyperchem/ Example] by Paul Bourke, and other [{{SVN Trunk}}Jmol-datafiles/hin/ example files].
 [[File formats/Formats/HIN|Details of HIN format]].

@@ Line 161: / Line 161: @@
 http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
-[http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/ Description] by Paul Bourke.
+[http://paulbourke.net/dataformats/cube/ Description] by Paul Bourke.
 [{{SVN Trunk}}Jmol-datafiles/cube/ Example files].