Downloads:

759

Downloads of v 1.13.1:

459

Last Update:

11/30/2018

Package Maintainer(s):

Software Author(s):

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

Tags:

chimera chemistry molecular modeling python nonsilent admin

UCSF Chimera

1.13.1 | Updated: 11/30/2018

Downloads:

759

Downloads of v 1.13.1:

459

Maintainer(s):

Software Author(s):

  • UCSF Resource for Biocomputing
  • Visualization
  • and Informatics

UCSF Chimera 1.13.1

All Checks are Passing

2 Passing Test


Validation Testing Passed


Verification Testing Passed

Details

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:

>

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

1. Ensure you are set for organizational deployment

Please see the organizational deployment guide

  • 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://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. Enter your internal repository url

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

4. Choose your deployment method:


choco upgrade chimera -y --source="'STEP 3 URL'" [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="'STEP 3 URL'" 
$exitCode = $LASTEXITCODE

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

Exit $exitCode

- name: Ensure chimera installed
  win_chocolatey:
    name: chimera
    state: present
    version: 1.13.1
    source: STEP 3 URL

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

Coming early 2020! Central Managment Reporting available now! More information...


chocolatey_package 'chimera' do
  action    :install
  version  '1.13.1'
  source   'STEP 3 URL'
end

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


Chocolatey::Ensure-Package
(
    Name: chimera,
    Version: 1.13.1,
    Source: STEP 3 URL
);

Requires Otter Chocolatey Extension. See docs at https://inedo.com/den/otter/chocolatey.


cChocoPackageInstaller chimera
{
   Name     = 'chimera'
   Ensure   = 'Present'
   Version  = '1.13.1'
   Source   = 'STEP 3 URL'
}

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


package { 'chimera':
  provider => 'chocolatey',
  ensure   => '1.13.1',
  source   => 'STEP 3 URL',
}

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


salt '*' chocolatey.install chimera version="1.13.1" source="STEP 3 URL"

See docs at https://docs.saltstack.com/en/latest/ref/modules/all/salt.modules.chocolatey.html.

5. 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 gep13 on 12/3/2018.

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    = 'e5fedc018f8889b30eda62fb3cb5ca281f75b1e4da8f09771248f7ef6cdf33a6'
   checksumType64= 'sha256'
   silentArgs   = '/VERYSILENT /SUPPRESSMSGBOXES /NORESTART /SP-'
   validExitCodes= @(0)
}

Install-ChocolateyPackage @packageArgs
tools\LICENSE.txt
From: http://www.cgl.ucsf.edu/chimera/license.html

LICENSE

UCSF Chimera Non-Commercial Software License Agreement

This license agreement ("License"), effective today, is made by and 
between you ("Licensee") and The Regents of the University of California, 
a California corporation having its statewide administrative offices at 
1111 Franklin Street, Oakland, California 94607-5200 ("The Regents"), 
acting through its Office of Innovation, Technology & Alliances, 
University of California San Francisco ("UCSF"), 3333 California Street, 
Suite S-11, San Francisco, California 94143, and concerns certain software 
known as "UCSF Chimera," a system of software programs for the 
visualization and interactive manipulation of molecular models, developed 
by the Computer Graphics Laboratory at UCSF for research purposes and 
includes executable code, source code, and documentation ("Software").

1. General. 
   A non-exclusive, nontransferable, perpetual license is granted to the 
   Licensee to install and use the Software for academic, non-profit, or 
   government-sponsored research purposes. Use of the Software under this 
   License is restricted to non-commercial purposes. Commercial use of 
   the Software requires a separately executed written license agreement.
2. Permitted Use and Restrictions. 
   Licensee agrees that it will use the Software, and any modifications, 
   improvements, or derivatives to the Software that the Licensee may 
   create (collectively, "Improvements") solely for internal, non-
   commercial purposes and shall not distribute or transfer the Software 
   or Improvements to any person or third parties without prior written 
   permission from The Regents. The term "non-commercial," as used in 
   this License, means academic or other scholarly research which (a) is 
   not undertaken for profit, or (b) is not intended to produce works, 
   services, or data for commercial use, or (c) is neither conducted, nor 
   funded, by a person or an entity engaged in the commercial use, 
   application or exploitation of works similar to the Software.
3. Ownership and Assignment of Copyright. 
   The Licensee acknowledges that The Regents hold copyright in the 
   Software and associated documentation, and the Software and associated 
   documentation are the property of The Regents. The Licensee agrees 
   that any Improvements made by Licensee shall be subject to the same 
   terms and conditions as the Software. Licensee agrees not to assert a 
   claim of infringement in Licensee copyrights in Improvements in the 
   event The Regents prepares substantially similar modifications or 
   derivative works. The Licensee agrees to use his/her reasonable best 
   efforts to protect the contents of the Software and to prevent 
   unauthorized disclosure by its agents, officers, employees, and 
   consultants. If the Licensee receives a request to furnish all or any 
   portion of the Software to a third party, Licensee will not fulfill 
   such a request but will refer the third party to the UCSF Chimera web 
   page so that the third party's use of this Software will be subject 
   to the terms and conditions of this License. Notwithstanding the 
   above, Licensee may disclose any Improvements that do not involve 
   disclosure of the Software.
4. Copies. 
   The Licensee may make a reasonable number of copies of the Software 
   for the purposes of backup, maintenance of the Software or the 
   development of derivative works based on the Software. These 
   additional copies shall carry the copyright notice and shall be 
   controlled by this License, and will be destroyed along with the 
   original by the Licensee upon termination of the License.
5. Acknowledgement. 
   Licensee agrees that any publication of results obtained with the 
   Software will acknowledge its use by an appropriate citation as 
   specified in the documentation.
6. Disclaimer of Warranties and Limitation of Liability. 
   THE LICENSEE AGREES THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, 
   BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND 
   FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. THE REGENTS MAKES NO 
   REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT INFRINGE ANY 
   PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE REGENTS BE 
   LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
   CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
   SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR 
   BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
   WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE 
   OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
   EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
7. Termination. 
   This License is effective until terminated by either party. Licensee's 
   rights under this License will terminate automatically without notice 
   from The Regents if Licensee fails to comply with any term(s) of this 
   License. Licensee may terminate the License by giving written notice 
   of termination to The Regents. Upon termination of this License, 
   Licensee shall immediately discontinue all use of the Software and 
   destroy the original and all copies, full or partial, of the Software, 
   including any modifications or derivative works, and associated 
   documentation.
8. Governing Law and General Provisions. 
   This License shall be governed by the laws of the State of California, 
   excluding the application of its conflicts of law rules. This License 
   shall not be governed by the United Nations Convention on Contracts 
   for the International Sale of Goods, the application of which is 
   expressly excluded. If any provisions of this License are held invalid 
   or unenforceable for any reason, the remaining provisions shall remain 
   in full force and effect. This License is binding upon any heirs and 
   assigns of the Licensee. The License granted to Licensee hereunder may 
   not be assigned or transferred to any other person or entity without 
   the express consent of The Regents. This License constitutes the 
   entire agreement between the parties with respect to the use of the 
   Software licensed hereunder and supersedes all other previous or 
   contemporaneous agreements or understandings between the parties, 
   whether verbal or written, concerning the subject matter. Any 
   translation of this License is done for local requirements and in the 
   event of a dispute between the English and any non-English versions, 
   the English version of this License shall govern. 

Revised 28jan04

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.

Version Downloads Last Updated Status
UCSF Chimera 1.13 97 Friday, August 3, 2018 Approved
UCSF Chimera 1.12 203 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