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| | + | {{Jmol_Documentation_Sections}} |
| | (An attempt to compile information on file format specifications. It's not complete yet.) | | (An attempt to compile information on file format specifications. It's not complete yet.) |
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| − | Jmol [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/ example/test data files] in all formats accepted. | + | Jmol [{{SVN Trunk}}Jmol-datafiles/ example/test data files] in all formats accepted. |
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| − | [http://en.wikipedia.org/wiki/Chemical_file_format Chemical file formats] on Wikipedia. | + | [[:en:Chemical_file_format|Chemical file formats]] on Wikipedia. |
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| | + | [http://openbabel.sourceforge.net/wiki/Category:Formats File formats] on Open Babel. |
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| − | = Coordinates of molecule =
| + | Nice description of [http://reference.wolfram.com/mathematica/guide/3DGeometryAndModelingFormats.html 3D Geometry & Modeling Formats] by Wolfram Mathematica. |
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| − | == (MDL) MOL and SD ==
| + | See the specific subsections: |
| − | Jmol reads MOL and SD files (and can write MOL files under some circumstances).
| + | <div style="width:30ex;"> |
| − | | + | {{File_Formats}} |
| − | Original from Elsevier MDL.
| + | </div> |
| − | | + | <div style="clear:both;"></div> |
| − | Official document: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf, copied [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/mol/ctfile.pdf here].
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| − | [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/mol/ Example files].
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| − | | |
| − | == PDB ==
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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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| − | [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/pdb/ Example files].
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| − | | |
| − | == XYZ ==
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| − | Jmol reads XYZ files.
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| − | [http://local.wasp.uwa.edu.au/~pbourke/dataformats/xyz/ Example] by Paul Bourke.
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| − | [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/xyz/ Example files].
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| − | | |
| − | == CIF ==
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| − | Jmol reads CIF files.
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| − | Crystallographic Information File, the official format from the International Union of Crystallography. [http://www.iucr.org/iucr-top/cif/standard/cifstd1.html Original documentation], Acta Cryst. (1991). A47, 655-685, and [http://www.iucr.org/iucr-top/cif/spec/version1.1/index.html 2003 update].
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| − | | |
| − | == mmCIF ==
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| − | Jmol reads mmCIF files.
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| − | Macromolecular Crystallographic Information File, an expanded format to cope with macromolecules.
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| − | [http://www.pdb.org/robohelp/ftp/files_formats/structures/chemical_component_format/chemical_component_mmcif_format.htm Official documentation].
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| − | | |
| − | == Gaussian ==
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| − | Gaussian input, output and log [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/gaussian/ example files].
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| − | | |
| − | | |
| − | == (Gaussian) Cube ==
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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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| − | | |
| − | Description of Cube Input and Cube Output formats:
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| − | http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
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| − | | |
| − | [http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/ Description] by Paul Bourke.
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| − | [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/cube/ Example files].
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| − | | |
| − | == (Hyperchem) HIV ==
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| − | Jmol reads HIV files.
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| − | [http://local.wasp.uwa.edu.au/~pbourke/dataformats/hyperchem/ Example] by Paul Bourke.
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| − | [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/hin/ Example files].
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| − | | |
| − | == (Tripos) Alchemy ==
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| − | Jmol reads Alchemy and Alchemy2000 files.
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| − | [http://local.wasp.uwa.edu.au/~pbourke/dataformats/alc/alc3/ Alchemy example] and [http://local.wasp.uwa.edu.au/~pbourke/dataformats/alc/ Alchemy2000 description] by Paul Bourke.
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| − | | |
| − | == GAMESS ==
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| − | Jmol reads GAMESS files (General Atomic and Molecular Electronic Structure System, by Gordon research group at Iowa State University).
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| − | | |
| − | [http://www.msg.ameslab.gov/GAMESS/doc.menu.html Official documentation].
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| − | | |
| − | = Surfaces =
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| − | | |
| − | == Jmol Voxel (JVXL) ==
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| − | Jmol reads and writes JVXL files.
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| − | | |
| − | This format is unique to Jmol, stores isosurface data.
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| − | | |
| − | Documented at http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf
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| − | | |
| − | == Pmesh ==
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| − | Jmol reads pmesh files for rendering pmesh surfaces, using not the <code>load</code> command, but the <code>pmesh</code> command.
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| − | [http://www.stolaf.edu/academics/chemapps/jmol/docs/#pmesh Description].
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| − | Example files [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/pmesh/ _1_] and [http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/10x10pmesh.txt _2_].
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| − | == (Gaussian) Cube ==
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| − | | |
| − | See [[#(Gaussian)_Cube|above]].
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| − | | |
| − | = Scripting =
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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.
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