Difference between revisions of "File formats"

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(A timid attempt to compile information on file format specifications. It's far from complete yet.)
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{{Jmol_Documentation_Sections}}
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(An attempt to compile information on file format specifications. It's not complete yet.)
  
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== (Gaussian) Cube format ==
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Jmol [{{SVN Trunk}}Jmol-datafiles/ example/test data files] in all formats accepted.
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Jmol reads Cube files.
 
  
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Original from Gaussian software ([http://www.gaussian.com/ Gaussian website]).
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[[:en:Chemical_file_format|Chemical file formats]] on Wikipedia.
  
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Description of Cube Input and Cube Output formats:
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[http://openbabel.sourceforge.net/wiki/Category:Formats File formats] on Open Babel.
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http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
 
  
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Nice description of [http://reference.wolfram.com/mathematica/guide/3DGeometryAndModelingFormats.html 3D Geometry & Modeling Formats] by Wolfram Mathematica.
  
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== Jmol Voxel (JVXL) format ==
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See the specific subsections:
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Jmol reads and writes JVXL files.
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<div style="width:30ex;">
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{{File_Formats}}
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Unique to Jmol, stores isosurface data.
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</div>
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<div style="clear:both;"></div>
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Documented at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf
 
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== MOL and SD formats ==
 
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Jmol reads MOL and SD files (and can write MOL files under some circumstances).
 
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Original from Elsevier MDL.
 
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Official document: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf
 
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== PDB format ==
 
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Jmol reads PDB files.
 
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(Official Protein Data Bank document) Atomic Coordinate Entry Format Description:
 
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http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html
 
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== Script format ==
 
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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.
 
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== Inline formats ==
 
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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).
 
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In turn, script commands can also be contained in the molecular file.
 
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To allow for this "inline" formats, several methods are implemented:
 
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''[Please, note that these are advanced procedures. For normal needs, they can be avoided in favour of using normal scripting practices.]''
 
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=== Molecular coordinates inline within a webpage ===
 
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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>.
 
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=== Molecular coordinates inline within a script or script file ===
 
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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).
 
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=== Script inline within a molecular coordinates file ===
 
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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:
 
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* In a PDB file, use <code>REMARK #jmolscript:</code> in any line, followed by the script commands in the same line.
 
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* In a MOL file, use <code>#jmolscript:</code> in the '''third line''', followed by the script commands in the same line. Note, however, that <code>#</code> cannot be the first character on that line, so use an initial '''space''' if nothing else.
 
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* In an XYZ file, use <code>#jmolscript:</code> in the '''second line''', followed by the script commands in the same line.
 
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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"