File formats
(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.
Coordinates of molecule
(MDL) MOL and SD
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, copied here.
PDB
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
XYZ
Jmol reads XYZ files. Example by Paul Bourke.
CIF
Jmol reads CIF files. Crystallographic Information File, the official format from the International Union of Crystallography. Original documentation, Acta Cryst. (1991). A47, 655-685, and 2003 update.
mmCIF
Jmol reads mmCIF files. Macromolecular Crystallographic Information File, an expanded format to cope with macromolecules. Official documentation.
Gaussian
Jmol reads only the output format. There are example files of Gaussian input, output and log.
(Gaussian) Cube
Jmol reads Cube files, original from Gaussian software (Gaussian website).
Description of Cube Input and Cube Output formats: http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
Description by Paul Bourke.
(Hyperchem) HIV
Jmol reads HIV files, the native format of Hyperchem, a software sold by Hypercube Inc..
Example by Paul Bourke, and other example files.
(Tripos) Alchemy
Jmol reads Alchemy and Alchemy2000 files. Alchemy example and Alchemy2000 description by Paul Bourke.
GAMESS
Jmol reads GAMESS files (General Atomic and Molecular Electronic Structure System, by Gordon research group at Iowa State University).
MOPAC
Jmol reads mopout output files from MOPAC and the new graphf output from MOPAC2007 (.mgf files), which contains coordinates, charges, and molecular orbitals.
openMOPAC, Molecular Orbital PACkage, public domain.
Images
Saving images from Jmol application
Images (snapshots) of Jmol's viewport, including the model in the current rendering, can be saved by using the application's top menu bar:
File > Export > Export Image or Script
and in the Image Type drop-down list, choose among JPEG, PNG or PPM formats, write a filename and click on Save.
Information on these image formats on Wikipedia.
Saving images from Jmol applet
Note: This only works for certain browsers, so it is not a general solution for the general user. In particular, it does not work in MSIE. In Firefox, it may fail for large applet sizes.
The command from the console or via JavaScript is
getProperty image.
The result is a base-64 encoded JPEG image that looks like this:
/9j/4AAQSkZJRgABAAAAAQABAAD//gBBSl...
Pop that into an <img> tag using Firefox or Opera (not MSIE), and you have
an image that you can copy into your clipboard and do anything you would
do with a JPG. The JavaScript required to create the tag looks like this:
var myImage = jmolGetPropertyAsString("image")
document.getElementById("someDiv").innerHTML =
'<img src="data:image/jpeg;base64,' + myImage + '">'
This is implemented in Bob Hanson's examples page. (Just under the applet, click on the word "image".)
Surfaces
Jmol Voxel (JVXL)
Jmol reads and writes JVXL files.
This format is unique to Jmol, stores isosurface data.
Documented at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf
Pmesh
Jmol reads pmesh files for rendering pmesh surfaces, using not the load command, but the pmesh command.
Description.
(Gaussian) Cube
See above.
Scripting
Script input
Jmol reads script files, using not the load command, but the script command. These are plain-text files containing commands in the Jmol scripting language (in part common with Rasmol and Chime), that will modify the way the molecular model is shown. The file can have any extension.
For details on the scripting language, visit the Interactive Scripting Documentation.
Script output
Jmol application (not the applet) can write a script file that will restore the current appearance and state of the model. This functionality is still under improvement.
Use the application's top menu bar:
File > Export > Export Image or Script
and in the Image Type drop-down list, choose SPT, write a filename and click on Save.
Inline formats
Molecular data are usually contained in an external file and loaded into Jmol using the load 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: jmolAppletInline, jmolLoadInline, jmolLoadInlineScript.
Molecular coordinates inline within a script or script file
Can be done using the data "model" command (Jmol 11 only).
Script inline within a molecular coordinates file
Scripts can be included after a #jmolscript: 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
REMARK #jmolscript:in any line, followed by the script commands in the same line. - In a MOL file, use
#jmolscript:in the third line, followed by the script commands in the same line. Note, however, that#cannot be the first character on that line, so use an initial space if nothing else. - In an XYZ file, use
#jmolscript: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.
Contributors
AngelHerraez, NicolasVervelle, Mkubasik, Geoffr, Pimpim, Dandin1
