Downloads:

2,831

Downloads of v 1.15:

107

Last Update:

03 Jan 2021

Package Maintainer(s):

Software Author(s):

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

Tags:

chimera chemistry molecular modeling python nonsilent admin

UCSF Chimera

This is not the latest version of UCSF Chimera available.

  • 1
  • 2
  • 3

1.15 | Updated: 03 Jan 2021

Downloads:

2,831

Downloads of v 1.15:

107

Maintainer(s):

Software Author(s):

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

  • 1
  • 2
  • 3
UCSF Chimera 1.15

This is not the latest version of UCSF Chimera 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

Deployment Method: Individual Install, Upgrade, & Uninstall

To install UCSF Chimera, run the following command from the command line or from PowerShell:

>

To upgrade UCSF Chimera, run the following command from the command line or from PowerShell:

>

To uninstall UCSF Chimera, 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 chimera -y --source="'INTERNAL REPO URL'" --version="'1.15'" [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 chimera -y --source="'INTERNAL REPO URL'" --version="'1.15'" 
$exitCode = $LASTEXITCODE

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

Exit $exitCode

- name: Install chimera
  win_chocolatey:
    name: chimera
    version: '1.15'
    source: INTERNAL REPO URL
    state: present

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


chocolatey_package 'chimera' do
  action    :install
  source   'INTERNAL REPO URL'
  version  '1.15'
end

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


cChocoPackageInstaller chimera
{
    Name     = "chimera"
    Version  = "1.15"
    Source   = "INTERNAL REPO URL"
}

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


package { 'chimera':
  ensure   => '1.15',
  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.

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

This package was approved by moderator flcdrg on 16 Jan 2021.

Description

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).

Non-Commercial use ONLY

Use of the Chimera is restricted to non-commercial, personal, academic, non-profit, or government-sponsored research purposes. Commercial use of the Software requires a separately executed written license agreement.


tools\chocolateyinstall.ps1
$ErrorActionPreference = 'Stop'

$BaseURL = 'https://www.cgl.ucsf.edu'

# Discovering download link
# Process found here:  https://stackoverflow.com/questions/34422255/
# Unsure if all settings are needed.
$url = "$BaseURL/chimera/cgi-bin/secure/chimera-get.py"
$postData = "choice=Accept&file=win64/chimera-$env:ChocolateyPackageVersion-win64.exe"
$buffer = [text.encoding]::ascii.getbytes($postData)
[net.httpWebRequest] $req = [net.webRequest]::create($url)
$req.method = "POST"
$req.Accept = "text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8"
$req.Headers.Add("Accept-Language: en-US")
$req.Headers.Add("Accept-Encoding: gzip,deflate")
$req.Headers.Add("Accept-Charset: ISO-8859-1,utf-8;q=0.7,*;q=0.7")
$req.AllowAutoRedirect = $false
$req.ContentType = "application/x-www-form-urlencoded"
$req.ContentLength = $buffer.length
$req.TimeOut = 50000
$req.KeepAlive = $true
$req.Headers.Add("Keep-Alive: 300");
$reqst = $req.getRequestStream()
$reqst.write($buffer, 0, $buffer.length)
$reqst.flush()
$reqst.close()
[net.httpWebResponse] $res = $req.getResponse()
$resst = $res.getResponseStream()
$sr = new-object IO.StreamReader($resst)
$result = $sr.ReadToEnd()
$res.close()

$URLstub = ($result.split() |? {$_ -match 'href='}) -replace '.*href="(.*)".*','$1'

Write-Host 'You are establishing a license agreement as defined here:' -ForegroundColor Cyan
Write-Host 'http://www.cgl.ucsf.edu/chimera/license.html' -ForegroundColor Cyan

$packageArgs = @{
   packageName   = $env:ChocolateyPackageName
   fileType      = 'EXE'
   url64bit      = $BaseURL + $URLstub
   softwareName  = 'UCSF Chimera*' 
   checksum64    = '98a7f234bb99c22448fb82767ead4ef76e7cb039a87d89f6d752dcf7379914ce'
   checksumType64= 'sha256'
   silentArgs   = '/VERYSILENT /SUPPRESSMSGBOXES /NORESTART /SP-'
   validExitCodes= @(0)
}

Install-ChocolateyPackage @packageArgs

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
UCSF Chimera 1.15 107 Sunday, January 3, 2021 Approved
UCSF Chimera 1.14 900 Friday, December 6, 2019 Approved
UCSF Chimera 1.13.1 614 Friday, November 30, 2018 Approved
UCSF Chimera 1.13 199 Friday, August 3, 2018 Approved
UCSF Chimera 1.12 303 Thursday, February 22, 2018 Approved

This package has no dependencies.

Discussion for the UCSF Chimera Package

Ground Rules:

  • This discussion is only about UCSF Chimera and the UCSF Chimera 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 UCSF Chimera, 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.
comments powered by Disqus