Difference between revisions of "File formats"

From Jmol
Jump to navigation Jump to search
m (→‎Molecular coordinates inline within a script or script file)
m
 
(67 intermediate revisions by 7 users not shown)
Line 1: Line 1:
−
(A timid attempt to compile information on file format specifications. It's far from complete yet.)
+
{{Jmol_Documentation_Sections}}
 +
(An attempt to compile information on file format specifications. It's not complete yet.)
  
−
== (Gaussian) Cube format ==
+
Jmol [{{SVN Trunk}}Jmol-datafiles/ example/test data files] in all formats accepted.
−
Jmol reads Cube files.
 
  
−
Original from Gaussian software ([http://www.gaussian.com/ Gaussian website]).
+
[[:en:Chemical_file_format|Chemical file formats]] on Wikipedia.
  
−
Description of Cube Input and Cube Output formats:
+
[http://openbabel.sourceforge.net/wiki/Category:Formats File formats] on Open Babel.
−
http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
 
  
 +
Nice description of [http://reference.wolfram.com/mathematica/guide/3DGeometryAndModelingFormats.html 3D Geometry & Modeling Formats] by Wolfram Mathematica.
  
−
== Jmol Voxel (JVXL) format ==
+
See the specific subsections:
−
Jmol reads and writes JVXL files.
+
<div style="width:30ex;">
−
 
+
{{File_Formats}}
−
Unique to Jmol, stores isosurface data.
+
</div>
−
 
+
<div style="clear:both;"></div>
−
Documented at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf
 
−
 
 
−
 
 
−
== MOL and SD formats ==
 
−
Jmol reads MOL and SD files (and can write MOL files under some circumstances).
 
−
 
 
−
Original from Elsevier MDL.
 
−
 
 
−
Official document: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf
 
−
 
 
−
 
 
−
== PDB format ==
 
−
Jmol reads PDB files.
 
−
 
 
−
(Official Protein Data Bank document) Atomic Coordinate Entry Format Description:
 
−
http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html
 
−
 
 
−
 
 
−
== Script format ==
 
−
Jmol reads script files, using not the <code>load</code> command, but the <code>script</code> command. These are plain-text files containing commands in the Jmol/Rasmol/Chime syntax, that will modify the way the molecular model is shown. The file can have any extension.
 
−
 
 
−
 
 
−
== Inline formats ==
 
−
Molecular data are usually contained in an external file and loaded into Jmol using the <code>load</code> command, but they can also be contained within the webpage (or fed into it using JavaScript or PHP, e.g. from a database).
 
−
 
 
−
In turn, script commands can also be contained in the molecular file.
 
−
 
 
−
To allow for this "inline" formats, several methods are implemented:
 
−
 
 
−
''[Please, note that these are advanced procedures. For normal needs, they can be avoided in favour of using normal scripting practices.]''
 
−
 
 
−
=== Molecular coordinates inline within a webpage ===
 
−
Can be done using direct instructions for the applet or, more easily, using functions in the Jmol.js library: <code>[http://jmol.org/jslibrary/#jmolAppletInline jmolAppletInline], [http://jmol.org/jslibrary/#jmolLoadInline jmolLoadInline], [http://jmol.org/jslibrary/#jmolLoadInlineScript jmolLoadInlineScript]</code>.
 
−
 
 
−
=== Molecular coordinates inline within a script or script file ===
 
−
Can be done using the <code>[http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#data data "model"]</code> command (Jmol 11 only).
 
−
 
 
−
=== Script inline within a molecular coordinates file ===
 
−
Scripts can be included after a <code>#jmolscript:</code> tag (case-sensitive). This must be taken as a comment by the molecular file parser, so its location depends on the file format:
 
−
* In a PDB file, use <code>REMARK #jmolscript:</code> in any line, followed by the script commands in the same line.
 
−
* In a MOL file, use an initial '''space''' plus <code>#jmolscript:</code> in the '''third line''', followed by the script commands in the same line.
 
−
* In an XYZ file, use <code>#jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
 
−
 
 
−
In all cases, the script will be applied after the whole molecule has loaded.
 

Latest revision as of 22:56, 26 January 2020

Jmol + JSmol Documentation

(An attempt to compile information on file format specifications. It's not complete yet.)

Jmol example/test data files in all formats accepted.

Chemical file formats on Wikipedia.

File formats on Open Babel.

Nice description of 3D Geometry & Modeling Formats by Wolfram Mathematica.

See the specific subsections:

Contributors

AngelHerraez, NicolasVervelle, Mkubasik, Geoffr, Pimpim, Dandin1

Retrieved from "https://wiki.jmol.org/index.php?title=File_formats&oldid=10001"