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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. | | [http://openbabel.sourceforge.net/wiki/Category:Formats File formats] on Open Babel. |
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| | + | Nice description of [http://reference.wolfram.com/mathematica/guide/3DGeometryAndModelingFormats.html 3D Geometry & Modeling Formats] by Wolfram Mathematica. |
| | | | |
| − | = Coordinates of molecule =
| + | See the specific subsections: |
| − | | + | <div style="width:30ex;"> |
| − | == (MDL) MOL and SD ==
| + | {{File_Formats}} |
| − | Jmol reads MOL and SD files (and can write MOL files under some circumstances).
| + | </div> |
| − | Original from Elsevier MDL.
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| − | Contains atom coordinates and bonds. Limited to 1000 atoms.
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| − | | |
| − | 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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| − | | |
| − | | |
| − | == (Sybyl) MOL2 ==
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| − | Jmol reads MOL2 files.
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| − | Original from Tripos.
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| − | Contains atom coordinates, bonds, partial charge, substructure information.
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| − | | |
| − | Official document: http://www.tripos.com/data/support/mol2.pdf
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| − | | |
| − | | |
| − | == PDB ==
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| − | Jmol reads PDB files.
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| − | Contains atom coordinates and information on biomolecular residues, sequence, chains, hydrogen and disulfide bonds, secondary structure, biologically relevant sites, cofactors. Can also contain temperature factor, formal charge, element symbol, alternate locations.
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| − | | |
| − | (Official Protein Data Bank document) Atomic Coordinate Entry Format.
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| − | Description:
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| − | http://www.wwpdb.org/documentation/format23/v2.3.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. Originally from XMol package, but has been widely adopted by many other programs. Contains only atom coordinates.
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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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| − | Jmol reads only the output format.
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| − | There are
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| − | [http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/gaussian/ example files]
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| − | of Gaussian input, output and log.
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| − | | |
| − | | |
| − | == (Gaussian) Cube ==
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| − | Jmol reads Cube files, 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, the native format of Hyperchem, a software sold by [http://www.hyper.com/ Hypercube Inc.].
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| − | | |
| − | [http://local.wasp.uwa.edu.au/~pbourke/dataformats/hyperchem/ Example] by Paul Bourke, and other [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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| − | | |
| − | | |
| − | == MOPAC ==
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| − | Jmol reads '''mopout''' output files from [http://openmopac.net/ MOPAC]
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| − | and the new '''graphf''' output from MOPAC2007 ('''.mgf''' files), which
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| − | contains coordinates, charges, and molecular orbitals.
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| − | | |
| − | openMOPAC, Molecular Orbital PACkage, public domain.
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| − | | |
| − | = Images =
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| − | | |
| − | == Saving images from Jmol application ==
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| − | Images (snapshots) of Jmol's viewport, including the model in the current rendering, can be saved by using the application's top menu bar:
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| − | <code>File > Export > Export Image or Script</code>
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| − | and in the <code>Image Type</code> drop-down list, choose among <code>JPEG</code>, <code>PNG</code> or <code>PPM</code> formats, write a filename and click on <code>Save</code>.
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| − | | |
| − | Information on these image formats on [http://en.wikipedia.org/wiki/Graphics_file_format Wikipedia].
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| − | | |
| − | == Saving images from Jmol applet ==
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| − | <i>Note:</i> 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.
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| − | | |
| − | The command from the console or via JavaScript is
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| − | <code>getProperty image</code>.
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| − | | |
| − | The result is a base-64 encoded JPEG image that looks like this:
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| − | <pre>/9j/4AAQSkZJRgABAAAAAQABAAD//gBBSl...</pre>
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| − | | |
| − | Pop that into an <code><img></code> tag using Firefox or Opera (not MSIE), and you have
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| − | an image that you can copy into your clipboard and do anything you would
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| − | do with a JPG. The JavaScript required to create the tag looks like this:
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| − | <pre>var myImage = jmolGetPropertyAsString("image") | |
| − | document.getElementById("someDiv").innerHTML =
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| − | '<img src="data:image/jpeg;base64,' + myImage + '">'</pre>
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| − | This is implemented in
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| − | [http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm Bob Hanson's examples page]. (Just under the applet, click on the word "image".)
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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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| − | | |
| − | | |
| − | == Open DX ==
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| − | | |
| − | Jmol (11.1.18 or later) reads DX files for rendering isosurfaces and color mapping.
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| − | DX contains three-dimensional scalar data; most frequently, isosurface and color by molecular electrostatic potential (MEP).
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| − | | |
| − | (Not to be confused with JCAMP-DX format, used for spectral vibrational data, which can be shown
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| − | using [http://jspecview.sourceforge.net/ JSpecView Applet] and [http://www.mdlchime.com MDL Chime].)
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| − | | |
| − | Open DX files are produced, among others, by [http://apbs.sourceforge.net/ APBS] (Adaptive Poisson-Boltzmann Solver).
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| − | APBS exists in standalone and web-server-based versions, and as a plug-in for [http://pymol.sourceforge.net/ PyMOL].
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| − | | |
| − | ''Technical:''
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| − | : DX, as Cube, defines a three-dimensional grid of points in space. At each point is a number (a "scalar value"). This set of point values is then used by Jmol to define an "isosurface" -- the surface separating points having values greater than a given cutoff from those that have a value less than a certain cutoff. A typical application is molecular orbitals. The <code>phase</code> parameter of the <code>isosurface</code> command allows bicolor rendering: one color for "points greater than x" and another color for "points less than -x".
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| − | : Jmol can read DX files and re-export them to much smaller JVXL files.
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| − | | |
| − | Generally a MEP data set is not used for the isosurface itself. Rather, it is used to map color onto another isosurface, usually some representation of the "molecular surface".
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| − | | |
| − | Bottom line is that we can now take molecular electrostatic potential data that were generated in PyMOL (requires the APBS plugin for PyMOL) and use them to color a surface generated in Jmol.
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| − | | |
| − | Documentation:
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| − | * [http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf Jmol interpretation of DX files and re-exporting into much smaller JVXL files]
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| − | * [http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format DX generation of MEP data by APBS]
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| − | * [http://www.opendx.org OpenDX specification and software package]
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| − | | |
| − | = Scripting =
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| − | | |
| − | == Script input ==
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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 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.
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| − | | |
| − | For details on the scripting language, visit the [http://www.stolaf.edu/academics/chemapps/jmol/docs/ Interactive Scripting Documentation].
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| − | | |
| − | == Script output ==
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| − | 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.
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| − | | |
| − | Use the application's top menu bar:
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| − | <code>File > Export > Export Image or Script</code>
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| − | and in the <code>Image Type</code> drop-down list, choose <code>SPT</code>, write a filename and click on <code>Save</code>.
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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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