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Jmol molecule viewer

14.20.8

Package test results are passing.

This package was approved as a trusted package on 10/19/2017.

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

Features

  • Free, open-source software licensed under the GNU Lesser General Public License
  • Applet, Application, and Systems Integration Component*
  • Multi-language
  • Cross-platform
  • Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, ...
  • High-performance 3D rendering with no hardware requirements
  • File formats (see also the file formats section within Jmol Wiki):

    • MOL MDL / Elsevier / Symyx structure (classic version V2000)

    • V3000 MDL / Elsevier / Symyx structure (new version V3000)

    • SDF MDL / Elsevier / Symyx structure (multiple models)

    • CTFile MDL / Elsevier / Symyx chemical table (generic)

    • CIF Crystallographic Information File - standard from the International Union of Crystallography

    • mmCIF Macromolecular Crystallographic Information File - standard from the International Union of Crystallography

    • CML Chemical Markup Language

    • PDB Protein Data Bank - Research Collaboratory for Structural Bioinformatics

    • XYZ XYZ format, XMol file - Minnesota Supercomputer Institute

    • XYZ+vib XYZ format with added vibrational vector information

    • XYZ-FAH XYZ format for [email protected]

    • MOL2 Sybyl, Tripos

    • Alchemy Tripos

    • CSF Fujitsu CAChe chemical structure, now Fujitsu Sygress

    • GAMESS General Atomic and Molecular Electronic Structure System output (both US and UK variants) - Gordon Research Group, Iowa State University

    • Gaussian Gaussian 94/98/03 output - Gaussian, Inc.

    • Cube Gaussian, Inc.

    • Ghemical The Ghemical computational chemistry package

    • MM1GP Ghemical molecular mechanics file

    • HIN HIN / HIV files from HyperChem - Hypercube, Inc.

    • Jaguar Schrodinger, LLC

    • MOLPRO Molpro output

    • MOPAC MOPAC 93/97/2002 output (public domain)

    • MGF MOPAC 2007 (v.7.101) graphf output (public domain)

    • NWCHEM NWChem output - Pacific Northwest National Laboratory

    • odydata Odyssey data - WaveFunction, Inc.

    • xodydata Odyssey XML data - WaveFunction, Inc.

    • QOUT Q-Chem, Inc.

    • SHELX Structural Chemistry Department, University of Göttingen (Germany)

    • SMOL Spartan data - Wavefunction, Inc.

    • spinput Spartan data - Wavefunction, Inc.

    • GRO Gromos87 format from GROMACS

    • PQR Modified pdb format including charge and radius

    • Amber The Amber package of molecular simulation programs

    • JME Java Molecular Editor - Peter Ertl

    • CASTEP The CASTEP software package, uses density functional theory

    • FHI-aims Full-potential / all-electron electronic structure theory with local orbitals - Fritz-Haber-Institut der Max-Planck-Gesellschaft

    • VASP VASP / VAMP / Vienna ab-initio simulation package

    • DGrid Miroslav Kohout, Max-Planck Institute

    • ADF ADF output - Amsterdam Density Functional

    • XSD Accelrys Materials Studio

    • AGL ArgusLab

    • DFT Wien2k

    • AMPAC AMPAC output - Semichem, Inc.

    • WebMO WebMO interface to computational chemistry packages

    • Molden Electron density / molecular orbitals

    • PSI3 Output files from the PSI3 suite of quantum chemical programs

    • CRYSTAL Output files from CRYSTAL, a computational tool for solid state chemistry and physics. Theoretical Chemistry Group, Univ. Torino, Italy.

  • Files which are compressed with gzip will automatically be decompressed
  • Animations
  • Vibrations
  • Surfaces
  • Orbitals
  • Support for unit cell and symmetry operations
  • Schematic shapes for secondary structures in biomolecules
  • Measurements of distance, angle, torsion angle
  • Support for RasMol/Chime scripting language
  • JavaScript support library (Jmol.js)
  • Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.

To install Jmol molecule viewer, run the following command from the command line or from PowerShell:

C:\> choco install jmol

To upgrade Jmol molecule viewer, run the following command from the command line or from PowerShell:

C:\> choco upgrade jmol

Files

Hide
  • tools\chocolateyInstall.ps1 Show
    $ErrorActionPreference = 'Stop'; # stop on all errors
    
    $ToolsDir   = Split-Path -parent $MyInvocation.MyCommand.Path
    $PackageDir = Split-Path -Parent $ToolsDir
    
    # Remove previous versions
    $Previous = Get-ChildItem $PackageDir -filter "jmol*" | ?{ $_.PSIsContainer }
    if ($Previous) {
       $Previous | % { Remove-Item $_.FullName -Recurse -Force }
    }
    
    $installArgs = @{
       packageName  = $env:ChocolateyPackageName
       FileFullPath = (Get-ChildItem $ToolsDir -Filter "*.zip").FullName
       Destination  = $PackageDir
    }
    
    Get-ChocolateyUnzip @installArgs
    
    $JavaExe = "$env:ProgramData\Oracle\Java\javapath\javaw.exe"
    $target = (Get-ChildItem $PackageDir -filter jmol.jar -Recurse).fullname
    $icon = Join-Path $PackageDir 'tools\Jmol_icon13.ico'
    $launcher = Join-Path $PackageDir 'Jmol Launcher.exe'
    $SGpath = Join-Path $env:ChocolateyInstall 'tools\shimgen.exe'
    
    & $SGpath -o $launcher -p $JavaExe -c "-jar '$target'" -i $icon --gui
    
    $shortcut = Join-Path ([Environment]::GetFolderPath("Desktop")) 'Jmol.lnk'
    
    Install-ChocolateyShortcut -ShortcutFilePath $shortcut -TargetPath $launcher -IconLocation $icon
    
  • tools\chocolateyUninstall.ps1 Show
    $desktop = [Environment]::GetFolderPath("Desktop")
    $shortcut = Join-Path $desktop 'Jmol.lnk'
     
    if ([System.IO.File]::Exists($shortcut)) {
        Write-Debug "Found the desktop shortcut. Deleting it..."
        [System.IO.File]::Delete($shortcut)
    }
    
  • tools\Jmol-14.20.8-binary.zip Show
    md5: B22D320AE39744D46F56CC2FB83E009A | sha1: 4FCE86BA284BEDDCBFFD46D302C6B7AF3D262924 | sha256: E0E9EB364BB1314F5E989619876B80E326BE78ADA3E4EDFB1953618B6B84334C | sha512: 1C307626AB87271F9DF0D081DDFB1852EEA30F951EFE561730799F8EA12B61799ACE0834336531C01B41D0E25E6A2BC892B018A1E259CEAB49DAE0D2BA06F9D6
  • tools\Jmol_icon13.ico
  • tools\LICENSE.txt Show
                       GNU LESSER GENERAL PUBLIC LICENSE
                           Version 3, 29 June 2007
    
     Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
     Everyone is permitted to copy and distribute verbatim copies
     of this license document, but changing it is not allowed.
    
    
      This version of the GNU Lesser General Public License incorporates
    the terms and conditions of version 3 of the GNU General Public
    License, supplemented by the additional permissions listed below.
    
      0. Additional Definitions.
    
      As used herein, "this License" refers to version 3 of the GNU Lesser
    General Public License, and the "GNU GPL" refers to version 3 of the GNU
    General Public License.
    
      "The Library" refers to a covered work governed by this License,
    other than an Application or a Combined Work as defined below.
    
      An "Application" is any work that makes use of an interface provided
    by the Library, but which is not otherwise based on the Library.
    Defining a subclass of a class defined by the Library is deemed a mode
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      A "Combined Work" is a work produced by combining or linking an
    Application with the Library.  The particular version of the Library
    with which the Combined Work was made is also called the "Linked
    Version".
    
      The "Minimal Corresponding Source" for a Combined Work means the
    Corresponding Source for the Combined Work, excluding any source code
    for portions of the Combined Work that, considered in isolation, are
    based on the Application, and not on the Linked Version.
    
      The "Corresponding Application Code" for a Combined Work means the
    object code and/or source code for the Application, including any data
    and utility programs needed for reproducing the Combined Work from the
    Application, but excluding the System Libraries of the Combined Work.
    
      1. Exception to Section 3 of the GNU GPL.
    
      You may convey a covered work under sections 3 and 4 of this License
    without being bound by section 3 of the GNU GPL.
    
      2. Conveying Modified Versions.
    
      If you modify a copy of the Library, and, in your modifications, a
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       a) under this License, provided that you make a good faith effort to
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       b) under the GNU GPL, with none of the additional permissions of
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      3. Object Code Incorporating Material from Library Header Files.
    
      The object code form of an Application may incorporate material from
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       the Library is used in it and that the Library and its use are
       covered by this License.
    
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       document.
    
       c) For a Combined Work that displays copyright notices during
       execution, include the copyright notice for the Library among
       these notices, as well as a reference directing the user to the
       copies of the GNU GPL and this license document.
    
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           0) Convey the Minimal Corresponding Source under the terms of this
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           recombine or relink the Application with a modified version of
           the Linked Version to produce a modified Combined Work, in the
           manner specified by section 6 of the GNU GPL for conveying
           Corresponding Source.
    
           1) Use a suitable shared library mechanism for linking with the
           Library.  A suitable mechanism is one that (a) uses at run time
           a copy of the Library already present on the user's computer
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           of the Library that is interface-compatible with the Linked
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       e) Provide Installation Information, but only if you would otherwise
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       Information in the manner specified by section 6 of the GNU GPL
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      5. Combined Libraries.
    
      You may place library facilities that are a work based on the
    Library side by side in a single library together with other library
    facilities that are not Applications and are not covered by this
    License, and convey such a combined library under terms of your
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       a) Accompany the combined library with a copy of the same work based
       on the Library, uncombined with any other library facilities,
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       b) Give prominent notice with the combined library that part of it
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       accompanying uncombined form of the same work.
    
      6. Revised Versions of the GNU Lesser General Public License.
    
      The Free Software Foundation may publish revised and/or new versions
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  • tools\VERIFICATION.txt Show
    VERIFICATION
    Verification is intended to assist the Chocolatey moderators and community
    in verifying that this package's contents are trustworthy.
     
    The installer is available from SourceForge:
    https://sourceforge.net/projects/jmol/files/Jmol-<Latest Version>-binary.zip
    
    Direct Download:
    
    Version  : 14.20.8
    URL      : https://sourceforge.net/projects/jmol/files/Jmol-14.20.8-binary.zip
    CheckSum : e0e9eb364bb1314f5e989619876b80e326be78ada3e4edfb1953618b6b84334c
    
    

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Dependencies

Maintainer(s)

Software Author(s)

  • The Jmol Development Team

Copyright

Copyright © 1998-2016 The Jmol Development Team

Tags

Release Notes

https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.20/Version%2014.20.8/

Version History

Version Downloads Last updated Status
Jmol molecule viewer 14.20.7 34 Thursday, October 5, 2017 approved
Jmol molecule viewer 14.20.6 71 Tuesday, September 19, 2017 approved
Jmol molecule viewer 14.20.5 498 Friday, September 1, 2017 approved
Jmol molecule viewer 14.20.3 2123 Tuesday, August 1, 2017 approved
Jmol molecule viewer 14.18.1 2100 Monday, June 12, 2017 approved
Jmol molecule viewer 14.17.1 538 Friday, June 2, 2017 approved
Jmol molecule viewer 14.15.2 2308 Wednesday, May 3, 2017 approved
Jmol molecule viewer 14.9.1 1715 Wednesday, March 8, 2017 approved
Jmol molecule viewer 14.8.0 685 Tuesday, January 31, 2017 approved
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