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Jmol molecule viewer

14.6.1.20160811

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This package was approved by moderator jberezanski on 8/24/2016.

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 --version 14.6.1.20160811

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

C:\> choco upgrade jmol --version 14.6.1.20160811

Files

Hide
  • tools\chocolateyInstall.ps1 Show 
    $packageName = 'jmol'
$MajorVersion = '14.6'
$MinorVersion = '14.6.1'
$SubVersion = '2016.08.11'

$installArgs = @{
   packageName = $packageName
   url = "https://sourceforge.net/projects/jmol/files/Jmol/Version%20$majorVersion/Version%20$MinorVersion/Jmol-$($MinorVersion)_$SubVersion-binary.zip/download"
   Checksum = '51683330ae480115f8c17a07166c2264645a6fa1'
   ChecksumType = 'sha1'
   UnzipLocation = $(Split-Path -parent $MyInvocation.MyCommand.Path)
}

Install-ChocolateyZipPackage @installArgs

$JavaExe = 'C:\ProgramData\Oracle\Java\javapath\javaw.exe'
$target = (Get-ChildItem $installArgs.UnzipLocation -filter jmol.jar -Recurse).fullname
$icon = Join-Path $installArgs.UnzipLocation "Jmol_icon13.ico"
$launcher = Join-Path $installArgs.UnzipLocation '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([Environment+SpecialFolder]::DesktopDirectory))
$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_icon13.ico

Virus Scan Results

In cases where actual malware is found, the packages are subject to removal. Software sometimes has false positives. Moderators do not necessarily validate the safety of the underlying software, only that a package retrieves software from the official distribution point and/or validate embedded software against official distribution point (where distribution rights allow redistribution).

Chocolatey Pro provides runtime protection from possible malware.

Dependencies

Package 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%2014.6/Version%2014.6.1/

Version History

Version Downloads Last updated Status
Jmol molecule viewer 14.29.29 3680 Friday, November 30, 2018 approved
Jmol molecule viewer 14.29.28 164 Thursday, November 1, 2018 approved
Jmol molecule viewer 14.29.26 121 Friday, October 12, 2018 approved
Jmol molecule viewer 14.29.22 545 Monday, September 17, 2018 approved
Jmol molecule viewer 14.29.17 9068 Friday, June 22, 2018 approved
Jmol molecule viewer 14.29.16 125 Friday, June 15, 2018 approved
Jmol molecule viewer 14.29.15 1401 Monday, May 28, 2018 approved
Jmol molecule viewer 14.29.14 150 Friday, May 18, 2018 approved
Jmol molecule viewer 14.29.13 3983 Tuesday, April 24, 2018 approved
Jmol molecule viewer 14.29.12 3369 Thursday, April 5, 2018 approved
Show More

Discussion for the Jmol molecule viewer Package

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  • This discussion is only about Jmol molecule viewer and the Jmol molecule viewer package. If you have feedback for Chocolatey, please contact the google group.
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  • Tell us what you love about the package or Jmol molecule viewer, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
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