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Downloads:

98,525

Downloads of v 14.20.3:

2,498

Last Update:

01 Aug 2017

Package Maintainer(s):

Software Author(s):

  • The Jmol Development Team

Tags:

jmol chemistry molecule rendering viewer java

Jmol molecule viewer

This is not the latest version of Jmol molecule viewer available.

  • 1
  • 2
  • 3

14.20.3 | Updated: 01 Aug 2017

Downloads:

98,525

Downloads of v 14.20.3:

2,498

Maintainer(s):

Software Author(s):

  • The Jmol Development Team

Jmol molecule viewer 14.20.3

This is not the latest version of Jmol molecule viewer available.

  • 1
  • 2
  • 3

All Checks are Passing

3 Passing Tests


Validation Testing Passed


Verification Testing Passed

Details

Scan Testing Successful:

No detections found in any package files

Details
Learn More

Deployment Method: Individual Install, Upgrade, & Uninstall

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

>

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

>

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

>

Deployment Method:

NOTE

This applies to both open source and commercial editions of Chocolatey.

1. Enter Your Internal Repository Url

(this should look similar to https://community.chocolatey.org/api/v2/)


2. Setup Your Environment

1. Ensure you are set for organizational deployment

Please see the organizational deployment guide

2. Get the package into your environment

  • Open Source or Commercial:
    • Proxy Repository - Create a proxy nuget repository on Nexus, Artifactory Pro, or a proxy Chocolatey repository on ProGet. Point your upstream to https://community.chocolatey.org/api/v2/. Packages cache on first access automatically. Make sure your choco clients are using your proxy repository as a source and NOT the default community repository. See source command for more information.
    • You can also just download the package and push it to a repository Download

3. Copy Your Script

choco upgrade jmol -y --source="'INTERNAL REPO URL'" --version="'14.20.3'" [other options]

See options you can pass to upgrade.

See best practices for scripting.

Add this to a PowerShell script or use a Batch script with tools and in places where you are calling directly to Chocolatey. If you are integrating, keep in mind enhanced exit codes.

If you do use a PowerShell script, use the following to ensure bad exit codes are shown as failures:


choco upgrade jmol -y --source="'INTERNAL REPO URL'" --version="'14.20.3'" 
$exitCode = $LASTEXITCODE

Write-Verbose "Exit code was $exitCode"
$validExitCodes = @(0, 1605, 1614, 1641, 3010)
if ($validExitCodes -contains $exitCode) {
  Exit 0
}

Exit $exitCode

- name: Install jmol
  win_chocolatey:
    name: jmol
    version: '14.20.3'
    source: INTERNAL REPO URL
    state: present

See docs at https://docs.ansible.com/ansible/latest/modules/win_chocolatey_module.html.


chocolatey_package 'jmol' do
  action    :install
  source   'INTERNAL REPO URL'
  version  '14.20.3'
end

See docs at https://docs.chef.io/resource_chocolatey_package.html.


cChocoPackageInstaller jmol
{
    Name     = "jmol"
    Version  = "14.20.3"
    Source   = "INTERNAL REPO URL"
}

Requires cChoco DSC Resource. See docs at https://github.com/chocolatey/cChoco.


package { 'jmol':
  ensure   => '14.20.3',
  provider => 'chocolatey',
  source   => 'INTERNAL REPO URL',
}

Requires Puppet Chocolatey Provider module. See docs at https://forge.puppet.com/puppetlabs/chocolatey.


4. If applicable - Chocolatey configuration/installation

See infrastructure management matrix for Chocolatey configuration elements and examples.

NOTE

Private CDN cached downloads available for licensed customers. Never experience 404 breakages again! Learn more...

Package Approved

This package was approved as a trusted package on 01 Aug 2017.

Description

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 Folding@home
    • 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.

tools\chocolateyInstall.ps1
$packageName = 'Jmol'

$url        = 'https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.20/Jmol%2014.20.3/Jmol-14.20.3-binary.zip'
$Checksum   = 'f0f2e7d007082df3a9e0501b6abf3a917209db96f1d2a6e93bbbbf75822605e6'
$installDir = Split-Path (Split-Path -parent $script:MyInvocation.MyCommand.Path)

$installArgs = @{
   packageName   = $packageName
   url           = $url
   Checksum      = $Checksum
   ChecksumType  = 'sha256'
   UnzipLocation = $installDir
}

Install-ChocolateyZipPackage @installArgs

$JavaExe = "$env:ProgramData\Oracle\Java\javapath\javaw.exe"
$target = (Get-ChildItem $installDir -filter jmol.jar -Recurse).fullname
$icon = Join-Path $installDir 'tools\Jmol_icon13.ico'
$launcher = Join-Path $installDir '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
$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_icon13.ico
 

Log in or click on link to see number of positives.

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.

Add to Builder Version Downloads Last Updated Status
Jmol molecule viewer 16.2.5 58 Tuesday, April 23, 2024 Approved
Jmol molecule viewer 16.2.1 45 Wednesday, April 10, 2024 Approved
Jmol molecule viewer 16.1.63 499 Wednesday, March 13, 2024 Approved
Jmol molecule viewer 16.1.57 97 Thursday, February 22, 2024 Approved
Jmol molecule viewer 16.1.49 122 Friday, January 26, 2024 Approved
Jmol molecule viewer 16.1.47 111 Monday, December 18, 2023 Approved
Jmol molecule viewer 16.1.45 118 Monday, November 13, 2023 Approved
Jmol molecule viewer 16.1.43 123 Saturday, October 28, 2023 Approved
Jmol molecule viewer 16.1.41 745 Tuesday, September 26, 2023 Approved
Jmol molecule viewer 16.1.35 379 Friday, August 25, 2023 Approved
Jmol molecule viewer 16.1.31 458 Saturday, August 5, 2023 Approved
Jmol molecule viewer 16.1.13 358 Friday, June 16, 2023 Approved
Jmol molecule viewer 16.1.11 372 Sunday, April 30, 2023 Approved
Jmol molecule viewer 16.1.9 179 Monday, April 3, 2023 Approved
Jmol molecule viewer 16.1.5 170 Saturday, February 18, 2023 Approved
Jmol molecule viewer 14.32.83 175 Sunday, January 8, 2023 Approved
Jmol molecule viewer 14.32.82 557 Friday, December 23, 2022 Approved
Jmol molecule viewer 14.32.81 348 Saturday, December 3, 2022 Approved
Jmol molecule viewer 14.32.80 146 Saturday, November 5, 2022 Approved
Jmol molecule viewer 14.32.77 156 Saturday, October 15, 2022 Approved
Jmol molecule viewer 14.32.75 296 Monday, September 26, 2022 Approved
Jmol molecule viewer 14.32.73 721 Tuesday, August 30, 2022 Approved
Jmol molecule viewer 14.32.68 154 Saturday, August 6, 2022 Approved
Jmol molecule viewer 14.32.63 143 Saturday, July 23, 2022 Approved
Jmol molecule viewer 14.32.62 133 Friday, July 8, 2022 Approved
Jmol molecule viewer 14.32.60 189 Friday, June 24, 2022 Approved
Jmol molecule viewer 14.32.58 227 Saturday, May 28, 2022 Approved
Jmol molecule viewer 14.32.55 172 Saturday, May 14, 2022 Approved
Jmol molecule viewer 14.32.54 171 Monday, May 2, 2022 Approved
Jmol molecule viewer 14.32.50 163 Tuesday, April 19, 2022 Approved
Jmol molecule viewer 14.32.42 183 Saturday, March 26, 2022 Approved
Jmol molecule viewer 14.32.33 178 Saturday, March 12, 2022 Approved
Jmol molecule viewer 14.32.26 162 Saturday, February 26, 2022 Approved
Jmol molecule viewer 14.32.21 166 Tuesday, February 15, 2022 Approved
Jmol molecule viewer 14.32.17 163 Wednesday, February 2, 2022 Approved
Jmol molecule viewer 14.32.10 181 Monday, January 10, 2022 Approved
Jmol molecule viewer 14.32.6 177 Wednesday, December 29, 2021 Approved
Jmol molecule viewer 14.31.61 213 Saturday, November 27, 2021 Approved
Jmol molecule viewer 14.31.60 187 Saturday, November 6, 2021 Approved
Jmol molecule viewer 14.31.57 200 Monday, October 18, 2021 Approved
Jmol molecule viewer 14.31.53 242 Wednesday, September 8, 2021 Approved
Jmol molecule viewer 14.31.52 174 Friday, August 20, 2021 Approved
Jmol molecule viewer 14.31.49 201 Saturday, August 7, 2021 Approved
Jmol molecule viewer 14.31.48 107 Sunday, August 1, 2021 Approved
Jmol molecule viewer 14.31.44 256 Monday, July 12, 2021 Approved
Jmol molecule viewer 14.31.41 245 Monday, May 31, 2021 Approved
Jmol molecule viewer 14.31.38 226 Saturday, May 15, 2021 Approved
Jmol molecule viewer 14.31.36 242 Sunday, April 18, 2021 Approved
Jmol molecule viewer 14.31.35 229 Monday, March 22, 2021 Approved
Jmol molecule viewer 14.31.32 311 Sunday, February 14, 2021 Approved
Jmol molecule viewer 14.31.28 216 Saturday, January 30, 2021 Approved
Jmol molecule viewer 14.31.23 254 Tuesday, January 12, 2021 Approved
Jmol molecule viewer 14.31.20 234 Sunday, December 27, 2020 Approved
Jmol molecule viewer 14.31.18 261 Friday, November 27, 2020 Approved
Jmol molecule viewer 14.31.17 273 Saturday, November 14, 2020 Approved
Jmol molecule viewer 14.31.10 273 Sunday, October 25, 2020 Approved
Jmol molecule viewer 14.31.9 277 Sunday, October 11, 2020 Approved
Jmol molecule viewer 14.31.8 285 Monday, September 28, 2020 Approved
Jmol molecule viewer 14.31.4 295 Saturday, September 12, 2020 Approved
Jmol molecule viewer 14.31.3 268 Sunday, August 30, 2020 Approved
Jmol molecule viewer 14.31.2 332 Sunday, July 19, 2020 Approved
Jmol molecule viewer 14.31.0 307 Wednesday, June 10, 2020 Approved
Jmol molecule viewer 14.30.2 529 Saturday, February 8, 2020 Approved
Jmol molecule viewer 14.30.1 422 Friday, December 20, 2019 Approved
Jmol molecule viewer 14.29.54 560 Saturday, October 12, 2019 Approved
Jmol molecule viewer 14.29.53 391 Saturday, September 28, 2019 Approved
Jmol molecule viewer 14.29.52 1655 Thursday, August 29, 2019 Approved
Jmol molecule viewer 14.29.47 1969 Wednesday, July 31, 2019 Approved
Jmol molecule viewer 14.29.46 919 Tuesday, June 18, 2019 Approved
Jmol molecule viewer 14.29.42 6993 Thursday, May 16, 2019 Approved
Jmol molecule viewer 14.29.40 3565 Tuesday, April 30, 2019 Approved
Jmol molecule viewer 14.29.36 3846 Sunday, April 14, 2019 Approved
Jmol molecule viewer 14.29.34 912 Thursday, April 11, 2019 Approved
Jmol molecule viewer 14.29.31 8839 Tuesday, March 5, 2019 Approved
Jmol molecule viewer 14.29.29 5960 Friday, November 30, 2018 Approved
Jmol molecule viewer 14.29.28 452 Thursday, November 1, 2018 Approved
Jmol molecule viewer 14.29.26 389 Friday, October 12, 2018 Approved
Jmol molecule viewer 14.29.22 821 Monday, September 17, 2018 Approved
Jmol molecule viewer 14.29.17 9403 Friday, June 22, 2018 Approved
Jmol molecule viewer 14.29.16 462 Friday, June 15, 2018 Approved
Jmol molecule viewer 14.29.15 1669 Monday, May 28, 2018 Approved
Jmol molecule viewer 14.29.14 449 Friday, May 18, 2018 Approved
Jmol molecule viewer 14.29.13 4232 Tuesday, April 24, 2018 Approved
Jmol molecule viewer 14.29.12 3633 Thursday, April 5, 2018 Approved
Jmol molecule viewer 14.29.5 7179 Monday, February 12, 2018 Approved
Jmol molecule viewer 14.28.3 506 Thursday, January 25, 2018 Approved
Jmol molecule viewer 14.28.2 444 Wednesday, January 17, 2018 Approved
Jmol molecule viewer 14.27.2 583 Friday, December 22, 2017 Approved
Jmol molecule viewer 14.25.2 787 Friday, December 1, 2017 Approved
Jmol molecule viewer 14.21.1 532 Tuesday, October 24, 2017 Approved
Jmol molecule viewer 14.20.8 483 Thursday, October 19, 2017 Approved
Jmol molecule viewer 14.20.7 453 Thursday, October 5, 2017 Approved
Jmol molecule viewer 14.20.6 447 Tuesday, September 19, 2017 Approved
Jmol molecule viewer 14.20.5 924 Friday, September 1, 2017 Approved
Jmol molecule viewer 14.20.3 2498 Tuesday, August 1, 2017 Approved
Jmol molecule viewer 14.18.1 2454 Monday, June 12, 2017 Approved
Jmol molecule viewer 14.17.1 908 Friday, June 2, 2017 Approved
Jmol molecule viewer 14.15.2 2660 Wednesday, May 3, 2017 Approved
Jmol molecule viewer 14.9.1 2085 Wednesday, March 8, 2017 Approved
Jmol molecule viewer 14.8.0 1033 Tuesday, January 31, 2017 Approved
Jmol molecule viewer 14.6.1.20160811 1031 Thursday, August 18, 2016 Approved
Jmol 14.4.4 450 Friday, April 22, 2016 Approved

Discussion for the Jmol molecule viewer Package

Ground Rules:

  • 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.
  • This discussion will carry over multiple versions. If you have a comment about a particular version, please note that in your comments.
  • The maintainers of this Chocolatey Package will be notified about new comments that are posted to this Disqus thread, however, it is NOT a guarantee that you will get a response. If you do not hear back from the maintainers after posting a message below, please follow up by using the link on the left side of this page or follow this link to contact maintainers. If you still hear nothing back, please follow the package triage process.
  • 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.
  • If you use a url, the comment will be flagged for moderation until you've been whitelisted. Disqus moderated comments are approved on a weekly schedule if not sooner. It could take between 1-5 days for your comment to show up.
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